### dukeUtaUncCrawford.txt wrangler notes for all submissions

select id,name,status, user_id from projects where name like "Duke%" or name like "UNC%" or name like "UTA%";
select id,name,status, user_id from projects where user_id = 17;
+-----+------------------------------------+------------+
| id  | name                               | status     |
+-----+------------------------------------+------------+
|  31 | Duke DNase-Seq GM12878 20081031    | displayed  |
|  32 | UNC FAIRE-Seq GM12878 20081031     | superceded |
|  33 | UTA ChIP-Seq CTCF GM12878 20081031 | superceded |
|  34 | UTA Input GM12878 20081031         | displayed  |
|  79 | Duke DNase-Seq GM12878 20081121    | displayed  |
|  80 | UNC FAIRE-Seq GM12878 20081121     | displayed  |
| 104 | Duke ExtraTracks 20081201          | displayed  |
| 109 | UTA Input K562 20081204            | displayed  |
| 112 | Duke DNase-Seq K562 20081206       | displayed  |
| 113 | UNC FAIRE-Seq K562 20081206        | displayed  |
| 114 | Duke DNase-Seq GM12878 20081208    | displayed  |
| 115 | UNC FAIRE-Seq GM12878 20081208     | displayed  |
| 116 | Duke DNase-Seq K562 20081208       | displayed  |
| 117 | UNC FAIRE-Seq K562 20081208        | displayed  |
| 127 | Duke DNase-Seq K562 20081210       | displayed  |
| 131 | Duke DNase-Seq GM12878 20081211    | displayed  |
| 228 | UTA ChIP-Seq CTCF GM12878 20090224 | displayed  |
| 231 | UNC FAIRE-Seq GM12878 20090224     | displayed  |
| 233 | Duke DNase-Seq GM12878 20090225    | displayed  |
| 234 | UNC FAIRE-Seq K562 20090225        | displayed  |
| 235 | Duke DNase-Seq K562 20090225       | displayed  |
| 244 | UTA ChIP-Seq CTCF K562 20090226    | displayed  |
| 245 | UTA ChIP-Seq c-Myc K562 20090226   | displayed  |
| 258 | Duke DNase-Seq GM12878 20090227    | displayed  |
| 272 | Duke DNase-Seq HepG2 20090310      | displayed  |
| 274 | UTA Input HepG2 20090312           | displayed  |
| 275 | UTA Input HelaS3 20090313          | displayed  |
| 278 | UTA ChIP Peaks Only                | displayed  |
| 280 | Duke DNase HelaS3 20090320         | displayed  |
| 281 | UTA ChIP-Seq CTCF HelaS3 20090320  | displayed  |
| 282 | UTA ChIP-Seq c-Myc HelaS3 20090320 | displayed  |
| 283 | UTA ChIP-Seq CTCF HepG2 20090320   | displayed  |
| 284 | UTA ChIP-Seq c-Myc HepG2 20090320  | displayed  |
| 285 | UNC FAIRE-Seq HelaS3 20090321      | displayed  |
| 286 | UNC FAIRE-Seq HepG2 20090323       | displayed  |
| 287 | UNC FAIRE-Seq Peaks Only 20090420  | displayed  |
+-----+------------------------------------+------------+
36 rows in set (0.00 sec)

Attempts at regeneration when Hive was out
==========================================
245 K562/c-Myc errors
Creating wiggle table definition in hg18.wgEncodeUtaChIPseqRawSignalRep1K562Cmyc
Saving /data/tmp/loadWig_hgwdev_409b_87ede0.tab
WARNING: Exceeded chr21 size 46944337 > 46944323. dropping 15 data point(s)
WARNING: Exceeded chr7 size 158821448 > 158821424. dropping 25 data point(s)
244 K562/Ctcf
Creating wiggle table definition in hg18.wgEncodeUtaChIPseqRawSignalRep3K562Ctcf
Saving /data/tmp/loadWig_hgwdev_4d01_89a820.tab
WARNING: Exceeded chr15 size 100338935 > 100338915. dropping 21 data point(s)
WARNING: Exceeded chr20 size 62435981 > 62435964. dropping 18 data point(s)
34 GM12878/Input
Creating wiggle table definition in hg18.wgEncodeUtaustinChIPseqRawSignalGm12878Input
Saving /data/tmp/loadWig_hgwdev_5073_45d160.tab
WARNING: Exceeded chr10 size 135374747 > 135374737. dropping 11 data point(s)
WARNING: Exceeded chr20 size 62435980 > 62435964. dropping 17 data point(s)
Creating wiggle table definition in hg18.wgEncodeUtaustinChIPseqSignalGm12878Input
Saving /data/tmp/loadWig_hgwdev_654a_466590.tab
WARNING: Exceeded chr10 size 135374747 > 135374737. dropping 11 data point(s)
WARNING: Exceeded chr20 size 62435980 > 62435964. dropping 17 data point(s)
109 K562/Input
Creating wiggle table definition in hg18.wgEncodeUtaustinChIPseqRawSignalK562Input
Saving /data/tmp/loadWig_hgwdev_7cac_8ca280.tab
WARNING: Exceeded chr10 size 135374738 > 135374737. dropping 2 data point(s)
Creating wiggle table definition in hg18.wgEncodeUtaustinChIPseqSignalK562Input
Saving /data/tmp/loadWig_hgwdev_6c0a_8bfa70.tab
WARNING: Exceeded chr10 size 135374738 > 135374737. dropping 2 data point(s)
113 K562/Input
Creating wiggle table definition in hg18.wgEncodeUncFAIREseqRawSignalRep2K562
Saving /data/tmp/loadWig_hgwdev_1fda_b8e650.tab
WARNING: Exceeded chr20 size 62435984 > 62435964. dropping 21 data point(s)
Creating wiggle table definition in hg18.wgEncodeUncFAIREseqRawSignalRep3K562
Saving /data/tmp/loadWig_hgwdev_cc0_b71960.tab
WARNING: Exceeded chr21 size 46944335 > 46944323. dropping 13 data point(s)
WARNING: Exceeded chr7 size 158821447 > 158821424. dropping 24 data point(s)

  Duke ExtraTracks 20081201          104
  Duke DNase-Seq HepG2 20090310      272
  Duke DNase-Seq GM12878 20090227    258(pk,sig,BO) 233*(Pk,Sig) 131(fastq) 114*(BO)  79*(BO) 31(taf,RawSig)
  Duke DNase-Seq K562 20090225       235(pk,sig) 127(fastq) 116(BO) 112(taf,RawSig)
  UTA Input GM12878 20081031          34
  UTA Input K562 20081204            109
  UTA Input HepG2 20090312           274
  UTA Input HelaS3 20090313          275
  UTA ChIP-Seq CTCF K562 20090226    244
  UTA ChIP-Seq c-Myc K562 20090226   245
  UTA ChIP-Seq CTCF GM12878 20090224 228(pk,sig,BO,RawSig,taf,fastq) 33*
  UNC FAIRE-Seq GM12878 20090224     231(pk,sig,BO,RawSig,taf,fastq) 115*(BO) 80*(BO) 32*(pk,sig,RawSig,taf,fastq)
  UNC FAIRE-Seq K562 20090225        234(pk,sig) 117(BO) 113(pk,sig,BO,RawSig,taf,fastq)

Duke Round 1
============
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/31 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/32 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/33 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/34 > validate_error 2>&1

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/31 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/32 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/33 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/34 > validate_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/31 > upload_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/32 > upload_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/33 > upload_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/34 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeLoad.pl -verbose 2 x /cluster/data/encode/pipeline/encpipeline_prod/31 > upload_error 2>&1 &

mysql> select avg(pValue),stddev(pValue),avg(pValue) + stddev(pValue),max(pValue),min(pValue),
       round(450*(min(pValue) - avg(pValue))/stddev(pValue))+550 minScore,
       round(450* stddev(pValue)            /stddev(pValue))+550 maxScore,
       round(450*(avg(pValue) - avg(pValue))/stddev(pValue))+550 midScore
from wgEncodeDukeDNaseSeqPeaksGm12878;
| avg(pValue)     | stddev(pValue)  | avg(pValue) + stddev(pValue) | max(pValue) | min(pValue)     | minScore | maxScore | midScore |
| 3.5181506516691 | 3.5025172998741 |              7.0206679515431 |          16 | 1.1799999475479 |      250 |     1000 |      550 |

  update wgEncodeDukeDNaseSeqPeaksGm12878 set score = 550 + round(450 *(pValue-avg(pValue))/stddev(pValue));
  update wgEncodeDukeDNaseSeqPeaksGm12878 set score = 550 + round(450 *(pValue-3.51815)/3.50252);
  update wgEncodeDukeDNaseSeqPeaksGm12878 set score = 1000 where score > 1000;

This gives a spread of scores between 100-1000 which centers on 550 and any pValue 1 or more sd above the mean is scored at 1000.

mysql> select min(score),avg(score),max(score)
from wgEncodeDukeDNaseSeqPeaksGm12878;
| min(score) | avg(score) | max(score) |
|        250 |   476.9985 |       1000 |



select min(
update p set score = 1000 where pValue >= 5;
update p set score = 300 + (700 * pValue/5) where pValue < 5;
CREATE TABLE encode_releases (
projectId	int(11),
trackName	varchar(255) not null,
downloadsDir	varchar(255),
type		varchar(20),
memtaData	varchar(255),
INDEX trackName, (projectId,trackName)) 

Duke 11-21
==========
cd 80;mv ../../ftp/prod/tsfurey//uncFAIREseqGM12878.20081121.tar.gz .
tar -xzf /uncFAIREseqGM12878.20081121.tar.gz &
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/80 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /cluster/data/encode/pipeline/encpipeline_prod/80 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/80 > upload_error 2>&1 &

cd 79;mv ../../ftp/prod/tsfurey//uncFAIREseqGM12878.20081121.tar.gz .
tar -xzf /uncFAIREseqGM12878.20081121.tar.gz &
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/79 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/79 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/79 > upload_error 2>&1 &

|  31 | Duke DNase-Seq GM12878 20081031         | displayed       |
|  79 | Duke DNase-Seq GM12878 20081121         | displayed       |
|  32 | UNC FAIRE-Seq GM12878 20081031          | displayed       |
|  80 | UNC FAIRE-Seq GM12878 20081121          | displayed       |
|  33 | UTA ChIP-Seq CTCF GM12878 20081031      | displayed       |
|  34 | UTA Input GM12878 20081031              | displayed       |
cd 31
/bin/gzip -c UCSC_submission/GM12878_DukeDNaseSeq.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878.narrowPeak.gz &                 
cd 32
/bin/gzip -c UCSC_submission/GM12878_UncFAIREseq.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeChromatinMap/wgEncodeUncFAIREseqPeaksGm12878.narrowPeak.gz &                  
cd 33
/bin/gzip -c UCSC_submission/GM12878_UtaChIPseq_CTCF.pk > /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878Ctcf.narrowPeak.gz &               

Duke Extra Tracks
=================
awk '{printf "%s\t%s\t%s\t%s\t1000\t.\n",$1,$2,$3,$4;}' old/DukeDNaseSeq_RegionsExcluded.bed > DukeDNaseSeq_RegionsExcluded.bed
edit DukeExtraTracks.DAF
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/104 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/104 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/104 > upload_error 2>&1 &
/cluster/home/tdreszer/bin/scripts/doEncodeLoad.pl x -skipLoad /cluster/data/encode/pipeline/encpipeline_prod/104 > upload_error 2>&1 &

Duke BO reentry
===============
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/114 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/114 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/114 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/115 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/115 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/115 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/116 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/116 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/116 > upload_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/117 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/117 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/117 > upload_error 2>&1 &

Prepare for Duke
================

rename table wgEncodeDukeDNaseSeqBaseOverlapSignalGm12878 to save_wgEncodeDukeDNaseSeqBaseOverlapSignalGm12878;
rename table wgEncodeDukeDNaseSeqPeaksGm12878             to save_wgEncodeDukeDNaseSeqPeaksGm12878;
rename table wgEncodeDukeDNaseSeqRawSignalRep1Gm12878     to save_wgEncodeDukeDNaseSeqRawSignalRep1Gm12878;
rename table wgEncodeDukeDNaseSeqRawSignalRep2Gm12878     to save_wgEncodeDukeDNaseSeqRawSignalRep2Gm12878;
rename table wgEncodeDukeDNaseSeqRawSignalRep3Gm12878     to save_wgEncodeDukeDNaseSeqRawSignalRep3Gm12878;
rename table wgEncodeDukeDNaseSeqRegionsExcludedGm12878   to save_wgEncodeDukeDNaseSeqRegionsExcludedGm12878;
rename table wgEncodeDukeDNaseSeqSignalGm12878            to save_wgEncodeDukeDNaseSeqSignalGm12878;
rename table wgEncodeDukeDnasePeaksGM12878                to save_wgEncodeDukeDnasePeaksGM12878;
rename table wgEncodeDukeDnaseSignalGM12878               to save_wgEncodeDukeDnaseSignalGM12878;
rename table wgEncodeDukeDNaseSeqBaseOverlapSignalK562    to save_wgEncodeDukeDNaseSeqBaseOverlapSignalK562;
rename table wgEncodeUncFAIREseqBaseOverlapSignalGm12878  to save_wgEncodeUncFAIREseqBaseOverlapSignalGm12878;
rename table wgEncodeUncFAIREseqPeaksGm12878              to save_wgEncodeUncFAIREseqPeaksGm12878;
rename table wgEncodeUncFAIREseqRawSignalRep1Gm12878      to save_wgEncodeUncFAIREseqRawSignalRep1Gm12878;
rename table wgEncodeUncFAIREseqRawSignalRep2Gm12878      to save_wgEncodeUncFAIREseqRawSignalRep2Gm12878;
rename table wgEncodeUncFAIREseqRawSignalRep3Gm12878      to save_wgEncodeUncFAIREseqRawSignalRep3Gm12878;
rename table wgEncodeUncFAIREseqSignalGm12878             to save_wgEncodeUncFAIREseqSignalGm12878;
rename table wgEncodeDukeDNaseSeqPeaksK562                to save_wgEncodeDukeDNaseSeqPeaksK562;
rename table wgEncodeDukeDNaseSeqRawSignalRep1K562        to save_wgEncodeDukeDNaseSeqRawSignalRep1K562;
rename table wgEncodeDukeDNaseSeqRawSignalRep2K562        to save_wgEncodeDukeDNaseSeqRawSignalRep2K562;
rename table wgEncodeDukeDNaseSeqRawSignalRep3K562        to save_wgEncodeDukeDNaseSeqRawSignalRep3K562;
rename table wgEncodeDukeDNaseSeqSignalK562               to save_wgEncodeDukeDNaseSeqSignalK562;
rename table wgEncodeUncFAIREseqBaseOverlapSignalK562     to save_wgEncodeUncFAIREseqBaseOverlapSignalK562;
rename table wgEncodeUncFAIREseqPeaksK562                 to save_wgEncodeUncFAIREseqPeaksK562;
rename table wgEncodeUncFAIREseqRawSignalRep1K562         to save_wgEncodeUncFAIREseqRawSignalRep1K562;
rename table wgEncodeUncFAIREseqRawSignalRep2K562         to save_wgEncodeUncFAIREseqRawSignalRep2K562;
rename table wgEncodeUncFAIREseqRawSignalRep3K562         to save_wgEncodeUncFAIREseqRawSignalRep3K562;
rename table wgEncodeUncFAIREseqSignalK562                to save_wgEncodeUncFAIREseqSignalK562;
rename table wgEncodeUtaChIPseqPeaksGm12878Ctcf           to save_wgEncodeUtaChIPseqPeaksGm12878Ctcf;
rename table wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf   to save_wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf;
rename table wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf   to save_wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf;
rename table wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf   to save_wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf;
rename table wgEncodeUtaChIPseqSignalGm12878Ctcf          to save_wgEncodeUtaChIPseqSignalGm12878Ctcf;
show tables like "save_%";
+---------------------------------------------------+
| Tables_in_hg18 (save_%)                           |
+---------------------------------------------------+
| save_wgEncodeDukeDNaseSeqBaseOverlapSignalGm12878 |
| save_wgEncodeDukeDNaseSeqBaseOverlapSignalK562    |
| save_wgEncodeDukeDNaseSeqPeaksGm12878             |
| save_wgEncodeDukeDNaseSeqPeaksK562                |
| save_wgEncodeDukeDNaseSeqRawSignalRep1Gm12878     |
| save_wgEncodeDukeDNaseSeqRawSignalRep1K562        |
| save_wgEncodeDukeDNaseSeqRawSignalRep2Gm12878     |
| save_wgEncodeDukeDNaseSeqRawSignalRep2K562        |
| save_wgEncodeDukeDNaseSeqRawSignalRep3Gm12878     |
| save_wgEncodeDukeDNaseSeqRawSignalRep3K562        |
| save_wgEncodeDukeDNaseSeqRegionsExcludedGm12878   |
| save_wgEncodeDukeDNaseSeqSignalGm12878            |
| save_wgEncodeDukeDNaseSeqSignalK562               |
| save_wgEncodeDukeDnasePeaksGM12878                |
| save_wgEncodeDukeDnaseSignalGM12878               |
| save_wgEncodeUncFAIREseqBaseOverlapSignalGm12878  |
| save_wgEncodeUncFAIREseqBaseOverlapSignalK562     |
| save_wgEncodeUncFAIREseqPeaksGm12878              |
| save_wgEncodeUncFAIREseqPeaksK562                 |
| save_wgEncodeUncFAIREseqRawSignalRep1Gm12878      |
| save_wgEncodeUncFAIREseqRawSignalRep1K562         |
| save_wgEncodeUncFAIREseqRawSignalRep2Gm12878      |
| save_wgEncodeUncFAIREseqRawSignalRep2K562         |
| save_wgEncodeUncFAIREseqRawSignalRep3Gm12878      |
| save_wgEncodeUncFAIREseqRawSignalRep3K562         |
| save_wgEncodeUncFAIREseqSignalGm12878             |
| save_wgEncodeUncFAIREseqSignalK562                |
| save_wgEncodeUtaChIPseqPeaksGm12878Ctcf           |
| save_wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf   |
| save_wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf   |
| save_wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf   |
| save_wgEncodeUtaChIPseqSignalGm12878Ctcf          |
+---------------------------------------------------+
Duke
====
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /hive/groups/encode/dcc/pipeline/encpipeline_prod/231 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/231 > load_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /hive/groups/encode/dcc/pipeline/encpipeline_prod/233 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/233 > load_error 2>&1 &

Now revert:
show tables like "%wgEncodeDukeDNaseSeqPeaksGm12878";
drop table save_wgEncodeDukeDNaseSeqPeaksGm12878; 
drop table deleted_wgEncodeDukeDNaseSeqPeaksGm12878; 
show tables like "%wgEncodeDukeDNaseSeqSignalGm12878";
drop table save_wgEncodeDukeDNaseSeqSignalGm12878; 
rename table save_wgEncodeDukeDNaseSeqBaseOverlapSignalGm12878 to wgEncodeDukeDNaseSeqBaseOverlapSignalGm12878;
rename table save_wgEncodeDukeDNaseSeqRawSignalRep1Gm12878     to wgEncodeDukeDNaseSeqRawSignalRep1Gm12878;
rename table save_wgEncodeDukeDNaseSeqRawSignalRep2Gm12878     to wgEncodeDukeDNaseSeqRawSignalRep2Gm12878;
rename table save_wgEncodeDukeDNaseSeqRawSignalRep3Gm12878     to wgEncodeDukeDNaseSeqRawSignalRep3Gm12878;

show tables like "%wgEncodeUncFAIREseqBaseOverlapSignalGm12878";
drop table save_wgEncodeUncFAIREseqBaseOverlapSignalGm12878;
show tables like "%wgEncodeUncFAIREseqPeaksGm12878";
drop table save_wgEncodeUncFAIREseqPeaksGm12878;
show tables like "%wgEncodeUncFAIREseqRawSignalRep1Gm12878";
drop table save_wgEncodeUncFAIREseqRawSignalRep1Gm12878;
show tables like "%wgEncodeUncFAIREseqRawSignalRep2Gm12878";
drop table save_wgEncodeUncFAIREseqRawSignalRep2Gm12878;
show tables like "%wgEncodeUncFAIREseqRawSignalRep3Gm12878";
drop table save_wgEncodeUncFAIREseqRawSignalRep3Gm12878;
show tables like "%wgEncodeUncFAIREseqSignalGm12878";
drop table save_wgEncodeUncFAIREseqSignalGm12878;

show tables like "%wgEncodeUncFAIREseqPeaksK562";
drop table save_wgEncodeUncFAIREseqPeaksK562;
show tables like "%wgEncodeUncFAIREseqSignalK562";
drop table save_wgEncodeUncFAIREseqSignalK562;
show tables like "%wgEncodeUncFAIREseqBaseOverlapSignalK562";
rename table save_wgEncodeUncFAIREseqBaseOverlapSignalK562 to wgEncodeUncFAIREseqBaseOverlapSignalK562;
show tables like "%wgEncodeUncFAIREseqRawSignalRep1K562";
rename table save_wgEncodeUncFAIREseqRawSignalRep1K562 to wgEncodeUncFAIREseqRawSignalRep1K562;
show tables like "%wgEncodeUncFAIREseqRawSignalRep2K562";
rename table save_wgEncodeUncFAIREseqRawSignalRep2K562 to wgEncodeUncFAIREseqRawSignalRep2K562;
show tables like "%wgEncodeUncFAIREseqRawSignalRep3K562";
rename table save_wgEncodeUncFAIREseqRawSignalRep3K562 to wgEncodeUncFAIREseqRawSignalRep3K562;

show tables like "%wgEncodeDukeDNaseSeqPeaksK562";
drop table save_wgEncodeDukeDNaseSeqPeaksK562;
show tables like "%wgEncodeDukeDNaseSeqSignalK562";
drop table save_wgEncodeDukeDNaseSeqSignalK562;
show tables like "%wgEncodeDukeDNaseSeqBaseOverlapSignalK562";
rename table save_wgEncodeDukeDNaseSeqBaseOverlapSignalK562 to wgEncodeDukeDNaseSeqBaseOverlapSignalK562;
show tables like "%wgEncodeDukeDNaseSeqRawSignalRep1K562";
rename table save_wgEncodeDukeDNaseSeqRawSignalRep1K562 to wgEncodeDukeDNaseSeqRawSignalRep1K562;
show tables like "%wgEncodeDukeDNaseSeqRawSignalRep2K562";
rename table save_wgEncodeDukeDNaseSeqRawSignalRep2K562 to wgEncodeDukeDNaseSeqRawSignalRep2K562;
show tables like "%wgEncodeDukeDNaseSeqRawSignalRep3K562";
rename table save_wgEncodeDukeDNaseSeqRawSignalRep3K562 to wgEncodeDukeDNaseSeqRawSignalRep3K562;

show tables like "%wgEncodeDukeDNaseSeqRegionsExcludedGm12878";
rename table save_wgEncodeDukeDNaseSeqRegionsExcludedGm12878 to wgEncodeDukeDNaseSeqRegionsExcludedGm12878;

show tables like "%wgEncodeUtaChIPseqPeaksGm12878Ctcf";
drop table save_wgEncodeUtaChIPseqPeaksGm12878Ctcf;
show tables like "%wgEncodeUtaChIPseqSignalGm12878Ctcf";
drop table save_wgEncodeUtaChIPseqSignalGm12878Ctcf;
show tables like "%wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf";
drop table save_wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf;
show tables like "%wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf";
drop table save_wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf;
show tables like "%wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf";
drop table save_wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf;

show tables like "%wgEncodeDukeDnasePeaksGM12878";
drop table save_wgEncodeDukeDnasePeaksGM12878;
show tables like "%wgEncodeDukeDnaseSignalGM12878";
drop table save_wgEncodeDukeDnaseSignalGM12878;
show tables like "save_%";
Empty set (0.09 sec)


Duke/UTA new submissions 2009-02-27
===================================
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation x /hive/groups/encode/dcc/pipeline/encpipeline_prod/245 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/245 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/245 > load_error 2>&1 &
/cluster/data/encode/pipeline/bin/encodeStatus.pl 245 loaded

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x /hive/groups/encode/dcc/pipeline/encpipeline_prod/258  validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /hive/groups/encode/dcc/pipeline/encpipeline_prod/258  validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/258 > load_error 2>&1 &
/cluster/data/encode/pipeline/bin/encodeStatus.pl 258 loaded

Duke
====
/cluster/data/encode/pipeline/bin/encodeStatus.pl 272 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 274 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 275 displayed


Duke Resubmits corrected Peaks 2009-03-20
=========================================
| wgEncodeDukeDNaseSeqNewPeaksGm12878     |
| wgEncodeDukeDNaseSeqNewPeaksHepg2       |
| wgEncodeDukeDNaseSeqNewPeaksK562        |
select count(*) from wgEncodeDukeDNaseSeqNewPeaksGm12878;|    97097 |
select count(*) from wgEncodeDukeDNaseSeqNewPeaksHepg2;  |   118945 |
select count(*) from wgEncodeDukeDNaseSeqNewPeaksK562;   |   106767 |
select count(*) from wgEncodeDukeDNaseSeqPeaksGm12878;   |    97097 |
select count(*) from wgEncodeDukeDNaseSeqPeaksHepg2;     |   118945 |
select count(*) from wgEncodeDukeDNaseSeqPeaksK562;      |   106767 |

SELECT DISTINCT t1.name FROM wgEncodeDukeDNaseSeqNewPeaksGm12878 t1, wgEncodeDukeDNaseSeqPeaksGm12878 t2 WHERE t1.name=t2.name and t1.chromEnd = (t2.chromEnd + 1) limit 2;

rename table wgEncodeDukeDNaseSeqPeaksGm12878 to wgEncodeOldDukeDNaseSeqPeaksGm12878;
rename table wgEncodeDukeDNaseSeqPeaksHepg2 to wgEncodeOldDukeDNaseSeqPeaksHepg2;
rename table wgEncodeDukeDNaseSeqPeaksK562 to wgEncodeOldDukeDNaseSeqPeaksK562;

rename table wgEncodeDukeDNaseSeqNewPeaksGm12878 to wgEncodeDukeDNaseSeqPeaksGm12878;
rename table wgEncodeDukeDNaseSeqNewPeaksHepg2 to wgEncodeDukeDNaseSeqPeaksHepg2;
rename table wgEncodeDukeDNaseSeqNewPeaksK562 to wgEncodeDukeDNaseSeqPeaksK562;

select count(*) from wgEncodeUtaChIPseqNewPeaksGm12878Ctcf; |    69505 |
select count(*) from wgEncodeUtaChIPseqNewPeaksK562Cmyc;    |    52589 |
select count(*) from wgEncodeUtaChIPseqNewPeaksK562Ctcf;    |    65337 |   
select count(*) from wgEncodeUtaChIPseqPeaksGm12878Ctcf;    |    69505 |
select count(*) from wgEncodeUtaChIPseqPeaksK562Cmyc;       |    52589 |
select count(*) from wgEncodeUtaChIPseqPeaksK562Ctcf;       |    65337 |

SELECT DISTINCT t1.name FROM wgEncodeUtaChIPseqNewPeaksGm12878Ctcf t1, wgEncodeUtaChIPseqPeaksGm12878Ctcf t2 WHERE t1.name=t2.name and t1.chromEnd = (t2.chromEnd + 1) limit 2;

rename table wgEncodeUtaChIPseqPeaksGm12878Ctcf to wgEncodeOldUtaChIPseqPeaksGm12878Ctcf; 
rename table wgEncodeUtaChIPseqPeaksK562Cmyc to wgEncodeOldUtaChIPseqPeaksK562Cmyc;    
rename table wgEncodeUtaChIPseqPeaksK562Ctcf to wgEncodeOldUtaChIPseqPeaksK562Ctcf; 

rename table wgEncodeUtaChIPseqNewPeaksGm12878Ctcf to wgEncodeUtaChIPseqPeaksGm12878Ctcf; 
rename table wgEncodeUtaChIPseqNewPeaksK562Cmyc to wgEncodeUtaChIPseqPeaksK562Cmyc;    
rename table wgEncodeUtaChIPseqNewPeaksK562Ctcf to wgEncodeUtaChIPseqPeaksK562Ctcf;

mv wgEncodeDukeDNaseSeqPeaksGm12878.narrowPeak.gz wgEncodeDukeDNaseSeqPeaksGm12878.narrowPeak.gz.old
mv wgEncodeDukeDNaseSeqPeaksK562.narrowPeak.gz      wgEncodeDukeDNaseSeqPeaksK562.narrowPeak.gz.old
mv wgEncodeDukeDNaseSeqPeaksHepg2.narrowPeak.gz     wgEncodeDukeDNaseSeqPeaksHepg2.narrowPeak.gz.old
mv wgEncodeUtaChIPseqPeaksGm12878Ctcf.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878Ctcf.narrowPeak.gz.old  
mv wgEncodeUtaChIPseqPeaksK562Ctcf.narrowPeak.gz    wgEncodeUtaChIPseqPeaksK562Ctcf.narrowPeak.gz.old
mv wgEncodeUtaChIPseqPeaksK562Cmyc.narrowPeak.gz    wgEncodeUtaChIPseqPeaksK562Cmyc.narrowPeak.gz.old 

mv wgEncodeDukeDNaseSeqNewPeaksGm12878.narrowPeak.gz   wgEncodeDukeDNaseSeqPeaksGm12878.narrowPeak.gz   
mv wgEncodeDukeDNaseSeqNewPeaksK562.narrowPeak.gz      wgEncodeDukeDNaseSeqPeaksK562.narrowPeak.gz
mv wgEncodeDukeDNaseSeqNewPeaksHepg2.narrowPeak.gz     wgEncodeDukeDNaseSeqPeaksHepg2.narrowPeak.gz
mv wgEncodeUtaChIPseqNewPeaksGm12878Ctcf.narrowPeak.gz wgEncodeUtaChIPseqPeaksGm12878Ctcf.narrowPeak.gz  
mv wgEncodeUtaChIPseqNewPeaksK562Ctcf.narrowPeak.gz    wgEncodeUtaChIPseqPeaksK562Ctcf.narrowPeak.gz
mv wgEncodeUtaChIPseqNewPeaksK562Cmyc.narrowPeak.gz    wgEncodeUtaChIPseqPeaksK562Cmyc.narrowPeak.gz 

/cluster/data/encode/pipeline/bin/encodeStatus.pl 277 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 278 displayed

/cluster/data/encode/pipeline/bin/encodeStatus.pl 280 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 281 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 282 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 283 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 284 displayed

Duke fix 285 hive crashed while loading 2009-03-21
==================================================
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/285 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl x -allowReloads /cluster/data/encode/pipeline/encpipeline_prod/285 > validate_error 2>&1 &

/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/285 > load_error 2>&1 &

Job died before Rep3,Peaks and fastq were loaded.  New DDF and restart.
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/285 >> load_error 2>&1 &

hg18 went down... start over on full set
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/285 > load_error 2>&1 &

Legitimate errors peaks and still no RawSiganlRep3, so start over excluding peaks
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/285 > load_error 2>&1 &

Edit load.ra and again...
/cluster/data/encode/pipeline/bin/encodeStatus.pl 285 loaded
/cluster/data/encode/pipeline/bin/encodeStatus.pl 285 displayed

More Duke/UNC/UTA 2009-04-20:
=============================
rename table wgEncodeUncFAIREseqPeaksGm12878 to wgEncodeOldUncFAIREseqPeaksGm12878;
rename table wgEncodeUncFAIREseqNewPeaksGm12878 to wgEncodeUncFAIREseqPeaksGm12878;
rename table wgEncodeUncFAIREseqPeaksK562 to wgEncodeOldUncFAIREseqPeaksK562;  
rename table wgEncodeUncFAIREseqNewPeaksK562 to wgEncodeUncFAIREseqPeaksK562;
/cluster/data/encode/pipeline/bin/encodeStatus.pl 287 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 286 displayed

Generate Raw Signals by our methods 2009-05-07
==============================================
# Created 4 DAF/DDF pairs:
rawSigDuke.D*F
rawSigUnc.D*F
rawSigUta.D*F
rawSigInput.D*F
# Contents of DDF has relative path to current tagAlign file (*.taf); and contents of DAF is only RawSignal and Alignments
cd encpipeline_prod
mkdir 2 (for test)
cd 2; cp rawSigDuke.D*F .

~/bin/scripts/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x ../2 > validate_error 2>&1
# no errors
~/bin/scripts/doEncodeValidate.pl -quick -skipAutoCreation x ../2 > validate_error 2>&1
view 'RawSignal' has already been loaded as track 'wgEncodeDukeDNaseSeqRawSignalRep2Gm12878'
show tables like "wgEncodeDuke%RawSignal%";
| wgEncodeDukeDNaseSeqRawSignalRep1Gm12878 |
| wgEncodeDukeDNaseSeqRawSignalRep1Helas3  |
| wgEncodeDukeDNaseSeqRawSignalRep1Hepg2   |
| wgEncodeDukeDNaseSeqRawSignalRep1K562    |
| wgEncodeDukeDNaseSeqRawSignalRep2Gm12878 |
| wgEncodeDukeDNaseSeqRawSignalRep2Helas3  |
| wgEncodeDukeDNaseSeqRawSignalRep2Hepg2   |
| wgEncodeDukeDNaseSeqRawSignalRep2K562    |
| wgEncodeDukeDNaseSeqRawSignalRep3Gm12878 |
| wgEncodeDukeDNaseSeqRawSignalRep3Helas3  |
| wgEncodeDukeDNaseSeqRawSignalRep3Hepg2   |
| wgEncodeDukeDNaseSeqRawSignalRep3K562    |
| wgEncodeUncFAIREseqRawSignalRep1Gm12878 |
| wgEncodeUncFAIREseqRawSignalRep1Helas3  |
| wgEncodeUncFAIREseqRawSignalRep1Hepg2   |
| wgEncodeUncFAIREseqRawSignalRep1K562    |
| wgEncodeUncFAIREseqRawSignalRep2Gm12878 |
| wgEncodeUncFAIREseqRawSignalRep2Helas3  |
| wgEncodeUncFAIREseqRawSignalRep2Hepg2   |
| wgEncodeUncFAIREseqRawSignalRep2K562    |
| wgEncodeUncFAIREseqRawSignalRep3Gm12878 |
| wgEncodeUncFAIREseqRawSignalRep3Helas3  |
| wgEncodeUncFAIREseqRawSignalRep3Hepg2   |
| wgEncodeUncFAIREseqRawSignalRep3K562    |
| wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf   |
| wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc    |
| wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf    |
| wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc     |
| wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf     |
| wgEncodeUtaChIPseqRawSignalRep1K562Cmyc      |
| wgEncodeUtaChIPseqRawSignalRep1K562Ctcf      |
| wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf   |
| wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc    |
| wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf    |
| wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc     |
| wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf     |
| wgEncodeUtaChIPseqRawSignalRep2K562Cmyc      |
| wgEncodeUtaChIPseqRawSignalRep2K562Ctcf      |
| wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf   |
| wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc     |
| wgEncodeUtaChIPseqRawSignalRep3K562Cmyc      |
| wgEncodeUtaChIPseqRawSignalRep3K562Ctcf      |
| wgEncodeUtaustinChIPseqRawSignalGm12878Input |
| wgEncodeUtaustinChIPseqRawSignalHelas3Input  |
| wgEncodeUtaustinChIPseqRawSignalHepg2Input   |
| wgEncodeUtaustinChIPseqRawSignalK562Input    |

rename table wgEncodeDukeDNaseSeqRawSignalRep1Gm12878     to wgEncodeDukeDNaseSeqRawSignalRep1Gm12878_terry    ;
rename table wgEncodeDukeDNaseSeqRawSignalRep1Helas3      to wgEncodeDukeDNaseSeqRawSignalRep1Helas3_terry     ;
rename table wgEncodeDukeDNaseSeqRawSignalRep1Hepg2       to wgEncodeDukeDNaseSeqRawSignalRep1Hepg2_terry      ;
rename table wgEncodeDukeDNaseSeqRawSignalRep1K562        to wgEncodeDukeDNaseSeqRawSignalRep1K562_terry       ;
rename table wgEncodeDukeDNaseSeqRawSignalRep2Gm12878     to wgEncodeDukeDNaseSeqRawSignalRep2Gm12878_terry    ;
rename table wgEncodeDukeDNaseSeqRawSignalRep2Helas3      to wgEncodeDukeDNaseSeqRawSignalRep2Helas3_terry     ;
rename table wgEncodeDukeDNaseSeqRawSignalRep2Hepg2       to wgEncodeDukeDNaseSeqRawSignalRep2Hepg2_terry      ;
rename table wgEncodeDukeDNaseSeqRawSignalRep2K562        to wgEncodeDukeDNaseSeqRawSignalRep2K562_terry       ;
rename table wgEncodeDukeDNaseSeqRawSignalRep3Gm12878     to wgEncodeDukeDNaseSeqRawSignalRep3Gm12878_terry    ;
rename table wgEncodeDukeDNaseSeqRawSignalRep3Helas3      to wgEncodeDukeDNaseSeqRawSignalRep3Helas3_terry     ;
rename table wgEncodeDukeDNaseSeqRawSignalRep3Hepg2       to wgEncodeDukeDNaseSeqRawSignalRep3Hepg2_terry      ;
rename table wgEncodeDukeDNaseSeqRawSignalRep3K562        to wgEncodeDukeDNaseSeqRawSignalRep3K562_terry       ;
rename table wgEncodeUncFAIREseqRawSignalRep1Gm12878      to wgEncodeUncFAIREseqRawSignalRep1Gm12878_terry     ;
rename table wgEncodeUncFAIREseqRawSignalRep1Helas3       to wgEncodeUncFAIREseqRawSignalRep1Helas3_terry      ;
rename table wgEncodeUncFAIREseqRawSignalRep1Hepg2        to wgEncodeUncFAIREseqRawSignalRep1Hepg2_terry       ;
rename table wgEncodeUncFAIREseqRawSignalRep1K562         to wgEncodeUncFAIREseqRawSignalRep1K562_terry        ;
rename table wgEncodeUncFAIREseqRawSignalRep2Gm12878      to wgEncodeUncFAIREseqRawSignalRep2Gm12878_terry     ;
rename table wgEncodeUncFAIREseqRawSignalRep2Helas3       to wgEncodeUncFAIREseqRawSignalRep2Helas3_terry      ;
rename table wgEncodeUncFAIREseqRawSignalRep2Hepg2        to wgEncodeUncFAIREseqRawSignalRep2Hepg2_terry       ;
rename table wgEncodeUncFAIREseqRawSignalRep2K562         to wgEncodeUncFAIREseqRawSignalRep2K562_terry        ;
rename table wgEncodeUncFAIREseqRawSignalRep3Gm12878      to wgEncodeUncFAIREseqRawSignalRep3Gm12878_terry     ;
rename table wgEncodeUncFAIREseqRawSignalRep3Helas3       to wgEncodeUncFAIREseqRawSignalRep3Helas3_terry      ;
rename table wgEncodeUncFAIREseqRawSignalRep3Hepg2        to wgEncodeUncFAIREseqRawSignalRep3Hepg2_terry       ;
rename table wgEncodeUncFAIREseqRawSignalRep3K562         to wgEncodeUncFAIREseqRawSignalRep3K562_terry        ;
rename table wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf   to wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf_terry  ;
rename table wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc    to wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc_terry   ;
rename table wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf    to wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf_terry   ;
rename table wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc     to wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc_terry    ;
rename table wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf     to wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf_terry    ;
rename table wgEncodeUtaChIPseqRawSignalRep1K562Cmyc      to wgEncodeUtaChIPseqRawSignalRep1K562Cmyc_terry     ;
rename table wgEncodeUtaChIPseqRawSignalRep1K562Ctcf      to wgEncodeUtaChIPseqRawSignalRep1K562Ctcf_terry     ;
rename table wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf   to wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf_terry  ;
rename table wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc    to wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc_terry   ;
rename table wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf    to wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf_terry   ;
rename table wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc     to wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc_terry    ;
rename table wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf     to wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf_terry    ;
rename table wgEncodeUtaChIPseqRawSignalRep2K562Cmyc      to wgEncodeUtaChIPseqRawSignalRep2K562Cmyc_terry     ;
rename table wgEncodeUtaChIPseqRawSignalRep2K562Ctcf      to wgEncodeUtaChIPseqRawSignalRep2K562Ctcf_terry     ;
rename table wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf   to wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf_terry  ;
rename table wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc     to wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc_terry    ;
rename table wgEncodeUtaChIPseqRawSignalRep3K562Cmyc      to wgEncodeUtaChIPseqRawSignalRep3K562Cmyc_terry     ;
rename table wgEncodeUtaChIPseqRawSignalRep3K562Ctcf      to wgEncodeUtaChIPseqRawSignalRep3K562Ctcf_terry     ;
rename table wgEncodeUtaustinChIPseqRawSignalGm12878Input to wgEncodeUtaustinChIPseqRawSignalGm12878Input_terry;
rename table wgEncodeUtaustinChIPseqRawSignalHelas3Input  to wgEncodeUtaustinChIPseqRawSignalHelas3Input_terry ;
rename table wgEncodeUtaustinChIPseqRawSignalHepg2Input   to wgEncodeUtaustinChIPseqRawSignalHepg2Input_terry  ;
rename table wgEncodeUtaustinChIPseqRawSignalK562Input    to wgEncodeUtaustinChIPseqRawSignalK562Input_terry   ;
#### Remember that wigs have file name element, so rename doesn't work.  All will need to be deleted!

~/bin/scripts/doEncodeValidate.pl -quick -skipAutoCreation x ../2 > validate_error 2>&1
view 'RawSignal' has already been loaded as track 'wgEncodeDukeDNaseSeqRawSignalRep2Gm12878'
# Problem is that the tables are in the tdb
# so edit trackDb.wgEncode.ra commenting out RawSignals
~/bin/scripts/doEncodeValidate.pl -quick -skipAutoCreation x ../2 > validate_error 2>&1
# no errors

# Had used local version testing changes to code.  Checked in made install and now:
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick x ../2 > validate_error 2>&1 &

# remove test dir
cd ..;rm -rf 2

# prepare archives and submit them
tar -cpzf rawSigDuke.tgz rawSigDuke.D*F
tar -cpzf rawSigUnc.tgz rawSigUnc.D*F
tar -cpzf rawSigUta.tgz rawSigUta.D*F
tar -cpzf rawSigInput.tgz rawSigInput.D*F

# log on to submission pipeline website as tsfurey, create 4 new submission dirs, submitted the for tars
| 325 | Duke DNase RawSignal Gen 20090507    | validating       |
| 326 | UNC FAIRE-Seq RawSignal Gen 20090507 | upload requested |
| 327 | UTA ChIP-Seq RawSignal Gen 20090507  | upload requested |
| 328 | UTA Input RawSignal Gen 20090507     | upload requested |

Edit trackDb.wgEncode.ra replacing the old RawSignal tracks with the new ones.
/cluster/data/encode/pipeline/bin/encodeStatus.pl 325 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 326 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 327 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 328 displayed

Splitting Uniqueness tracks 2009-05-12
======================================
 wgEncodeDukeDNaseSeqUniqueness20bpGm12878 |
| wgEncodeDukeDNaseSeqUniqueness24bpGm12878 |
| wgEncodeDukeDNaseSeqUniqueness35bpGm12878
cd /gbdb/hg18/wib
mv /gbdb/hg18/wib/wgEncodeDukeDNaseSeqUniqueness20bpGm12878.wib /gbdb/hg18/wib/wgEncodeDukeUniqueness20bp.wib
mv /gbdb/hg18/wib/wgEncodeDukeDNaseSeqUniqueness24bpGm12878.wib /gbdb/hg18/wib/wgEncodeDukeUniqueness24bp.wib
mv /gbdb/hg18/wib/wgEncodeDukeDNaseSeqUniqueness35bpGm12878.wib /gbdb/hg18/wib/wgEncodeDukeUniqueness35bp.wib

update wgEncodeDukeDNaseSeqUniqueness20bpGm12878 set file = '/gbdb/hg18/wib/wgEncodeDukeUniqueness20bp.wib'; 
update wgEncodeDukeDNaseSeqUniqueness24bpGm12878 set file = '/gbdb/hg18/wib/wgEncodeDukeDUniqueness24bp.wib'; 
update wgEncodeDukeDNaseSeqUniqueness35bpGm12878 set file = '/gbdb/hg18/wib/wgEncodeDukeUniqueness35bp.wib'; 

rename table wgEncodeDukeDNaseSeqUniqueness20bpGm12878 to wgEncodeDukeUniqueness20bp;
rename table wgEncodeDukeDNaseSeqUniqueness24bpGm12878 to wgEncodeDukeUniqueness24bp;
rename table wgEncodeDukeDNaseSeqUniqueness35bpGm12878 to wgEncodeDukeUniqueness35bp;

rename table wgEncodeDukeDNaseSeqRegionsExcludedGm12878 to wgEncodeDukeRegionsExcluded;
# in donwloads dir
mv wgEncodeDukeDNaseSeqRegionsExcludedGm12878.bed6.gz wgEncodeDukeDNaseSeqRegionsExcluded.bed6.gz
mv wgEncodeDukeDNaseSeqUniqueness20bpGm12878.wig.gz wgEncodeDukeDNaseSeqUniqueness20bp.wig.gz
mv wgEncodeDukeDNaseSeqUniqueness24bpGm12878.wig.gz wgEncodeDukeDNaseSeqUniqueness24bp.wig.gz
mv wgEncodeDukeDNaseSeqUniqueness35bpGm12878.wig.gz wgEncodeDukeDNaseSeqUniqueness35bp.wig.gz

mv wgEncodeDukeDNaseSeqRegionsExcluded.bed6.gz wgEncodeDukeRegionsExcluded.bed6.gz
mv wgEncodeDukeDNaseSeqUniqueness20bp.wig.gz wgEncodeDukeUniqueness20bp.wig.gz
mv wgEncodeDukeDNaseSeqUniqueness24bp.wig.gz wgEncodeDukeUniqueness24bp.wig.gz
mv wgEncodeDukeDNaseSeqUniqueness35bp.wig.gz wgEncodeDukeUniqueness35bp.wig.gz


Getting ready for pushQ 2009-5-12
=================================
trackDb
wgEncodeDukeDNaseSeqBaseOverlapSignalGm12878
wgEncodeDukeDNaseSeqBaseOverlapSignalHelas3
wgEncodeDukeDNaseSeqBaseOverlapSignalHepg2
wgEncodeDukeDNaseSeqBaseOverlapSignalK562
wgEncodeDukeDNaseSeqPeaksGm12878
wgEncodeDukeDNaseSeqPeaksHelas3
wgEncodeDukeDNaseSeqPeaksHepg2
wgEncodeDukeDNaseSeqPeaksK562
wgEncodeDukeDNaseSeqRawSignalRep1Gm12878
wgEncodeDukeDNaseSeqRawSignalRep1Helas3
wgEncodeDukeDNaseSeqRawSignalRep1Hepg2
wgEncodeDukeDNaseSeqRawSignalRep1K562
wgEncodeDukeDNaseSeqRawSignalRep2Gm12878
wgEncodeDukeDNaseSeqRawSignalRep2Helas3
wgEncodeDukeDNaseSeqRawSignalRep2Hepg2
wgEncodeDukeDNaseSeqRawSignalRep2K562
wgEncodeDukeDNaseSeqRawSignalRep3Gm12878
wgEncodeDukeDNaseSeqRawSignalRep3Helas3
wgEncodeDukeDNaseSeqRawSignalRep3Hepg2
wgEncodeDukeDNaseSeqRawSignalRep3K562
wgEncodeDukeDNaseSeqSignalGm12878
wgEncodeDukeDNaseSeqSignalHelas3
wgEncodeDukeDNaseSeqSignalHepg2
wgEncodeDukeDNaseSeqSignalK562
wgEncodeDukeRegionsExcluded                 
wgEncodeUncFAIREseqBaseOverlapSignalGm12878
wgEncodeUncFAIREseqBaseOverlapSignalHelas3
wgEncodeUncFAIREseqBaseOverlapSignalHepg2
wgEncodeUncFAIREseqBaseOverlapSignalK562
wgEncodeUncFAIREseqPeaksGm12878
wgEncodeUncFAIREseqPeaksHepg2
wgEncodeUncFAIREseqPeaksK562
wgEncodeUncFAIREseqRawSignalRep1Gm12878
wgEncodeUncFAIREseqRawSignalRep1Helas3
wgEncodeUncFAIREseqRawSignalRep1Hepg2
wgEncodeUncFAIREseqRawSignalRep1K562
wgEncodeUncFAIREseqRawSignalRep2Gm12878
wgEncodeUncFAIREseqRawSignalRep2Helas3
wgEncodeUncFAIREseqRawSignalRep2Hepg2
wgEncodeUncFAIREseqRawSignalRep2K562
wgEncodeUncFAIREseqRawSignalRep3Gm12878
wgEncodeUncFAIREseqRawSignalRep3Helas3
wgEncodeUncFAIREseqRawSignalRep3Hepg2
wgEncodeUncFAIREseqRawSignalRep3K562
wgEncodeUncFAIREseqSignalGm12878
wgEncodeUncFAIREseqSignalHelas3
wgEncodeUncFAIREseqSignalHepg2
wgEncodeUncFAIREseqSignalK562              
wgEncodeUtaChIPseqBaseOverlapSignalGm12878Ctcf
wgEncodeUtaChIPseqBaseOverlapSignalHelas3Cmyc
wgEncodeUtaChIPseqBaseOverlapSignalHelas3Ctcf
wgEncodeUtaChIPseqBaseOverlapSignalHepg2Cmyc
wgEncodeUtaChIPseqBaseOverlapSignalHepg2Ctcf
wgEncodeUtaChIPseqBaseOverlapSignalK562Cmyc
wgEncodeUtaChIPseqBaseOverlapSignalK562Ctcf
wgEncodeUtaChIPseqPeaksGm12878Ctcf
wgEncodeUtaChIPseqPeaksHelas3Cmyc
wgEncodeUtaChIPseqPeaksHelas3Ctcf
wgEncodeUtaChIPseqPeaksHepg2Cmyc
wgEncodeUtaChIPseqPeaksHepg2Ctcf
wgEncodeUtaChIPseqPeaksK562Cmyc
wgEncodeUtaChIPseqPeaksK562Ctcf
wgEncodeUtaChIPseqRawSignalGm12878Input
wgEncodeUtaChIPseqRawSignalHelas3Input
wgEncodeUtaChIPseqRawSignalHepg2Input
wgEncodeUtaChIPseqRawSignalK562Input
wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf
wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc
wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf
wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc
wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf
wgEncodeUtaChIPseqRawSignalRep1K562Cmyc
wgEncodeUtaChIPseqRawSignalRep1K562Ctcf
wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf
wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc
wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf
wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc
wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf
wgEncodeUtaChIPseqRawSignalRep2K562Cmyc
wgEncodeUtaChIPseqRawSignalRep2K562Ctcf
wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf
wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc
wgEncodeUtaChIPseqRawSignalRep3K562Cmyc
wgEncodeUtaChIPseqRawSignalRep3K562Ctcf
wgEncodeUtaChIPseqSignalGm12878Ctcf
wgEncodeUtaChIPseqSignalHelas3Cmyc
wgEncodeUtaChIPseqSignalHelas3Ctcf
wgEncodeUtaChIPseqSignalHepg2Cmyc
wgEncodeUtaChIPseqSignalHepg2Ctcf
wgEncodeUtaChIPseqSignalK562Cmyc
wgEncodeUtaChIPseqSignalK562Ctcf
wgEncodeUtaustinChIPseqSignalGm12878Input
wgEncodeUtaustinChIPseqSignalHelas3Input
wgEncodeUtaustinChIPseqSignalHepg2Input
wgEncodeUtaustinChIPseqSignalK562Input        
NOTE: Missing HelaS3 Peaks!
NOTE: Missing GM12878/c-Myc
Note: All (non-input) have 2 reps except GM12878/CTCF,HepG2/c-Myc,K562/c-Myc,K562/CTCF

/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/index.html
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep1Gm12878.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep1Helas3.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep1Hepg2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep1K562.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep2Gm12878.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep2Helas3.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep2Hepg2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep2K562.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep3Gm12878.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep3Helas3.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep3Hepg2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqAlignmentsRep3K562.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqBaseOverlapSignalGm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqBaseOverlapSignalHelas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqBaseOverlapSignalHepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqBaseOverlapSignalK562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksGm12878.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksHelas3.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksHepg2.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqPeaksK562.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep1Gm12878.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep1Helas3.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep1Hepg2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep1K562.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep2Gm12878.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep2Helas3.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep2Hepg2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep2K562.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep3Gm12878.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep3Helas3.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep3Hepg2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawDataRep3K562.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqSignalGm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqSignalHelas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqSignalHepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqSignalK562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeRegionsExcluded.bed6.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep1Gm12878.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep1Helas3.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep1Hepg2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep1K562.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep2Gm12878.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep2Helas3.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep2Hepg2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep2K562.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep3Gm12878.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep3Helas3.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep3Hepg2.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqAlignmentsRep3K562.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqBaseOverlapSignalGm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqBaseOverlapSignalHelas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqBaseOverlapSignalHepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqBaseOverlapSignalK562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqPeaksGm12878.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqPeaksHepg2.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqPeaksK562.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep1Gm12878.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep1Helas3.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep1Hepg2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep1K562.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep2Gm12878.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep2Helas3.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep2Hepg2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep2K562.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep3Gm12878.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep3Helas3.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep3Hepg2.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawDataRep3K562.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqSignalGm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqSignalHelas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqSignalHepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqSignalK562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep1Gm12878Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep1Helas3Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep1Helas3Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep1Hepg2Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep1Hepg2Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep1K562Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep1K562Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep2Gm12878Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep2Helas3Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep2Helas3Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep2Hepg2Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep2Hepg2Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep2K562Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep2K562Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep3Gm12878Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep3Hepg2Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep3K562Cmyc.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqAlignmentsRep3K562Ctcf.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqBaseOverlapSignalGm12878Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqBaseOverlapSignalHelas3Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqBaseOverlapSignalHelas3Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqBaseOverlapSignalHepg2Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqBaseOverlapSignalHepg2Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqBaseOverlapSignalK562Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqBaseOverlapSignalK562Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksGm12878Ctcf.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksHelas3Cmyc.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksHelas3Ctcf.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksHepg2Cmyc.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksHepg2Ctcf.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksK562Cmyc.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqPeaksK562Ctcf.narrowPeak.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep1Gm12878Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep1Helas3Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep1Helas3Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep1Hepg2Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep1Hepg2Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep1K562Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep1K562Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep2Gm12878Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep2Helas3Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep2Helas3Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep2Hepg2Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep2Hepg2Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep2K562Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep2K562Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep3Gm12878Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep3Hepg2Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep3K562Cmyc.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawDataRep3K562Ctcf.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqSignalGm12878Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqSignalHelas3Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqSignalHelas3Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqSignalHepg2Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqSignalHepg2Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqSignalK562Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqSignalK562Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqAlignmentsGm12878Input.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqAlignmentsHelas3Input.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqAlignmentsHepg2Input.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqAlignmentsK562Input.tagAlign.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqRawDataGm12878Input.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqRawDataHelas3Input.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqRawDataHepg2Input.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqRawDataK562Input.fastq.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqSignalGm12878Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqSignalHelas3Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqSignalHepg2Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqSignalK562Input.wig.gz

# Not yet available
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep1Gm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep1Helas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep1Hepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep1K562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep2Gm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep2Helas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep2Hepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep2K562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep3Gm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep3Helas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep3Hepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeDukeDNaseSeqRawSignalRep3K562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep1Gm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep1Helas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep1Hepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep1K562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep2Gm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep2Helas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep2Hepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep2K562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep3Gm12878.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep3Helas3.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep3Hepg2.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUncFAIREseqRawSignalRep3K562.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep1K562Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep1K562Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep2K562Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep2K562Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep3K562Cmyc.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaChIPseqRawSignalRep3K562Ctcf.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqRawSignalGm12878Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqRawSignalHelas3Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqRawSignalHepg2Input.wig.gz
/usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap/wgEncodeUtaustinChIPseqRawSignalK562Input.wig.gz
/cluster/data/encode/pipeline/bin/encodeStatus.pl 12 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 31 approved 
/cluster/data/encode/pipeline/bin/encodeStatus.pl 34 approved         
/cluster/data/encode/pipeline/bin/encodeStatus.pl 79 approved 
/cluster/data/encode/pipeline/bin/encodeStatus.pl 80 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 109 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 112 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 113 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 114 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 115 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 116 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 117 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 127 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 131 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 228 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 231 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 233 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 234 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 235 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 244 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 245 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 258 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 272 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 274 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 275 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 278 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 280 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 281 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 282 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 283 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 284 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 285 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 286 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 287 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 325 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 326 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 327 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 328 approved
### Opps.  SOme have been superceded
update projects set status = "superceded" where id = 233;
update projects set status = "superceded" where id = 114;
update projects set status = "superceded" where id = 79;
update projects set status = "superceded" where id = 33;
update projects set status = "superceded" where id = 115;
update projects set status = "superceded" where id = 80;
update projects set status = "superceded" where id = 32;
# Move superceded dir out of the way:
cd encpipeline_prod
mkdir superceded
mv 233 superceded/
mv 114 superceded/
79 superceded/
mv 33 superceded/
mv 115 superceded/
mv 80 superceded/
mv 32 superceded/
mv 66 superceded/
mv 108 superceded/

# Not yet for uniqueness tracks:
| wgEncodeDukeUniqueness20bp                     |
| wgEncodeDukeUniqueness24bp                     |
| wgEncodeDukeUniqueness35bp                     |

/cluster/data/encode/pipeline/bin/encodeStatus.pl 104 approved

New ro reregnerate Raw Sigs 2009-05-22
======================================
drop table wgEncodeDukeDNaseSeqRawSignalRep1Gm12878_terry;       
drop table wgEncodeDukeDNaseSeqRawSignalRep1Helas3_terry ;       
drop table wgEncodeDukeDNaseSeqRawSignalRep1Hepg2_terry  ;       
drop table wgEncodeDukeDNaseSeqRawSignalRep1K562_terry   ;       
drop table wgEncodeDukeDNaseSeqRawSignalRep2Gm12878_terry;       
drop table wgEncodeDukeDNaseSeqRawSignalRep2Helas3_terry ;       
drop table wgEncodeDukeDNaseSeqRawSignalRep2Hepg2_terry  ;       
drop table wgEncodeDukeDNaseSeqRawSignalRep2K562_terry   ;       
drop table wgEncodeDukeDNaseSeqRawSignalRep3Gm12878_terry;       
drop table wgEncodeDukeDNaseSeqRawSignalRep3Helas3_terry ;       
drop table wgEncodeDukeDNaseSeqRawSignalRep3Hepg2_terry  ;       
drop table wgEncodeDukeDNaseSeqRawSignalRep3K562_terry   ;
drop table wgEncodeUncFAIREseqRawSignalRep1Gm12878_terry ;     
drop table wgEncodeUncFAIREseqRawSignalRep1Helas3_terry  ;     
drop table wgEncodeUncFAIREseqRawSignalRep1Hepg2_terry   ;     
drop table wgEncodeUncFAIREseqRawSignalRep1K562_terry    ;     
drop table wgEncodeUncFAIREseqRawSignalRep2Gm12878_terry ;     
drop table wgEncodeUncFAIREseqRawSignalRep2Helas3_terry  ;     
drop table wgEncodeUncFAIREseqRawSignalRep2Hepg2_terry   ;     
drop table wgEncodeUncFAIREseqRawSignalRep2K562_terry    ;     
drop table wgEncodeUncFAIREseqRawSignalRep3Gm12878_terry ;     
drop table wgEncodeUncFAIREseqRawSignalRep3Helas3_terry  ;     
drop table wgEncodeUncFAIREseqRawSignalRep3Hepg2_terry   ;     
drop table wgEncodeUncFAIREseqRawSignalRep3K562_terry    ;     
drop table wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf_terry;        
drop table wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc_terry ;        
drop table wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf_terry ;        
drop table wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc_terry  ;        
drop table wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf_terry  ;        
drop table wgEncodeUtaChIPseqRawSignalRep1K562Cmyc_terry   ;        
drop table wgEncodeUtaChIPseqRawSignalRep1K562Ctcf_terry   ;        
drop table wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf_terry;        
drop table wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc_terry ;        
drop table wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf_terry ;        
drop table wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc_terry  ;        
drop table wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf_terry  ;        
drop table wgEncodeUtaChIPseqRawSignalRep2K562Cmyc_terry   ;        
drop table wgEncodeUtaChIPseqRawSignalRep2K562Ctcf_terry   ;        
drop table wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf_terry;        
drop table wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc_terry  ;        
drop table wgEncodeUtaChIPseqRawSignalRep3K562Cmyc_terry   ;        
drop table wgEncodeUtaChIPseqRawSignalRep3K562Ctcf_terry   ;        
drop table wgEncodeUtaustinChIPseqRawSignalGm12878Input_terry   ;        
drop table wgEncodeUtaustinChIPseqRawSignalHelas3Input_terry    ;        
drop table wgEncodeUtaustinChIPseqRawSignalHepg2Input_terry     ;        
drop table wgEncodeUtaustinChIPseqRawSignalK562Input_terry      ;        
       
cd ../325; doEncodeValidate.pl -quick -allowReloads x ../325 > validate_errors 2>&1 &
cd ../326; doEncodeValidate.pl -quick -allowReloads x ../326 > validate_errors 2>&1 &
cd ../327; doEncodeValidate.pl -quick -allowReloads x ../327 > validate_errors 2>&1 &
cd ../328; doEncodeValidate.pl -quick -allowReloads x ../328 > validate_errors 2>&1 &
ll autoRawSignal?.bed 
psg doEnc
tail autoRawSignal3.bed
cd ../325; doEncodeLoad.pl x ../325 > load_error 2>&1 &
cd ../326; doEncodeLoad.pl x ../326 > load_error 2>&1 &
cd ../327; doEncodeLoad.pl x ../327 > load_error 2>&1 &
cd ../328; doEncodeLoad.pl x ../328 > load_error 2>&1 &

# OUCH all wer loaded with the submission dir appended to the tablename!!!
drop table wgEncodeDukeDNaseSeqRawSignalRep1Gm12878;
drop table wgEncodeDukeDNaseSeqRawSignalRep1Helas3 ;
drop table wgEncodeDukeDNaseSeqRawSignalRep1Hepg2  ;
drop table wgEncodeDukeDNaseSeqRawSignalRep1K562   ;
drop table wgEncodeDukeDNaseSeqRawSignalRep2Gm12878;
drop table wgEncodeDukeDNaseSeqRawSignalRep2Helas3 ;
drop table wgEncodeDukeDNaseSeqRawSignalRep2Hepg2  ;
drop table wgEncodeDukeDNaseSeqRawSignalRep2K562   ;
drop table wgEncodeDukeDNaseSeqRawSignalRep3Gm12878;
drop table wgEncodeDukeDNaseSeqRawSignalRep3Helas3 ;
drop table wgEncodeDukeDNaseSeqRawSignalRep3Hepg2  ;
drop table wgEncodeDukeDNaseSeqRawSignalRep3K562   ;

rename table wgEncodeDukeDNaseSeqRawSignalRep1Gm12878_325 to wgEncodeDukeDNaseSeqRawSignalRep1Gm12878;
rename table wgEncodeDukeDNaseSeqRawSignalRep1Helas3_325  to wgEncodeDukeDNaseSeqRawSignalRep1Helas3 ;
rename table wgEncodeDukeDNaseSeqRawSignalRep1Hepg2_325   to wgEncodeDukeDNaseSeqRawSignalRep1Hepg2  ;
rename table wgEncodeDukeDNaseSeqRawSignalRep1K562_325    to wgEncodeDukeDNaseSeqRawSignalRep1K562   ;
rename table wgEncodeDukeDNaseSeqRawSignalRep2Gm12878_325 to wgEncodeDukeDNaseSeqRawSignalRep2Gm12878;
rename table wgEncodeDukeDNaseSeqRawSignalRep2Helas3_325  to wgEncodeDukeDNaseSeqRawSignalRep2Helas3 ;
rename table wgEncodeDukeDNaseSeqRawSignalRep2Hepg2_325   to wgEncodeDukeDNaseSeqRawSignalRep2Hepg2  ;
rename table wgEncodeDukeDNaseSeqRawSignalRep2K562_325    to wgEncodeDukeDNaseSeqRawSignalRep2K562   ;
rename table wgEncodeDukeDNaseSeqRawSignalRep3Gm12878_325 to wgEncodeDukeDNaseSeqRawSignalRep3Gm12878;
rename table wgEncodeDukeDNaseSeqRawSignalRep3Helas3_325  to wgEncodeDukeDNaseSeqRawSignalRep3Helas3 ;
rename table wgEncodeDukeDNaseSeqRawSignalRep3Hepg2_325   to wgEncodeDukeDNaseSeqRawSignalRep3Hepg2  ;
rename table wgEncodeDukeDNaseSeqRawSignalRep3K562_325    to wgEncodeDukeDNaseSeqRawSignalRep3K562   ;

drop table wgEncodeUncFAIREseqRawSignalRep1Gm12878;
drop table wgEncodeUncFAIREseqRawSignalRep1Helas3 ;
drop table wgEncodeUncFAIREseqRawSignalRep1Hepg2  ;
drop table wgEncodeUncFAIREseqRawSignalRep1K562   ;
drop table wgEncodeUncFAIREseqRawSignalRep2Gm12878;
drop table wgEncodeUncFAIREseqRawSignalRep2Helas3 ;
drop table wgEncodeUncFAIREseqRawSignalRep2Hepg2  ;
drop table wgEncodeUncFAIREseqRawSignalRep2K562   ;
drop table wgEncodeUncFAIREseqRawSignalRep3Gm12878;
drop table wgEncodeUncFAIREseqRawSignalRep3Helas3 ;
drop table wgEncodeUncFAIREseqRawSignalRep3Hepg2  ;
drop table wgEncodeUncFAIREseqRawSignalRep3K562   ;

rename table wgEncodeUncFAIREseqRawSignalRep1Gm12878_326 to wgEncodeUncFAIREseqRawSignalRep1Gm12878;
rename table wgEncodeUncFAIREseqRawSignalRep1Helas3_326  to wgEncodeUncFAIREseqRawSignalRep1Helas3 ;
rename table wgEncodeUncFAIREseqRawSignalRep1Hepg2_326   to wgEncodeUncFAIREseqRawSignalRep1Hepg2  ;
rename table wgEncodeUncFAIREseqRawSignalRep1K562_326    to wgEncodeUncFAIREseqRawSignalRep1K562   ;
rename table wgEncodeUncFAIREseqRawSignalRep2Gm12878_326 to wgEncodeUncFAIREseqRawSignalRep2Gm12878;
rename table wgEncodeUncFAIREseqRawSignalRep2Helas3_326  to wgEncodeUncFAIREseqRawSignalRep2Helas3 ;
rename table wgEncodeUncFAIREseqRawSignalRep2Hepg2_326   to wgEncodeUncFAIREseqRawSignalRep2Hepg2  ;
rename table wgEncodeUncFAIREseqRawSignalRep2K562_326    to wgEncodeUncFAIREseqRawSignalRep2K562   ;
rename table wgEncodeUncFAIREseqRawSignalRep3Gm12878_326 to wgEncodeUncFAIREseqRawSignalRep3Gm12878;
rename table wgEncodeUncFAIREseqRawSignalRep3Helas3_326  to wgEncodeUncFAIREseqRawSignalRep3Helas3 ;
rename table wgEncodeUncFAIREseqRawSignalRep3Hepg2_326   to wgEncodeUncFAIREseqRawSignalRep3Hepg2  ;
rename table wgEncodeUncFAIREseqRawSignalRep3K562_326    to wgEncodeUncFAIREseqRawSignalRep3K562   ;

drop table wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf;
drop table wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc ;
drop table wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf ;
drop table wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc  ;
drop table wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf  ;
drop table wgEncodeUtaChIPseqRawSignalRep1K562Cmyc   ;
drop table wgEncodeUtaChIPseqRawSignalRep1K562Ctcf   ;
drop table wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf;
drop table wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc ;
drop table wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf ;
drop table wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc  ;
drop table wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf  ;
drop table wgEncodeUtaChIPseqRawSignalRep2K562Cmyc   ;
drop table wgEncodeUtaChIPseqRawSignalRep2K562Ctcf   ;
drop table wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf;
drop table wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc  ;
drop table wgEncodeUtaChIPseqRawSignalRep3K562Cmyc   ;
drop table wgEncodeUtaChIPseqRawSignalRep3K562Ctcf   ;
                                                     
rename table wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf_327 to wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf;
rename table wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc_327  to wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc ;
rename table wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf_327  to wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf ;
rename table wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc_327   to wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc  ;
rename table wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf_327   to wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf  ;
rename table wgEncodeUtaChIPseqRawSignalRep1K562Cmyc_327    to wgEncodeUtaChIPseqRawSignalRep1K562Cmyc   ;
rename table wgEncodeUtaChIPseqRawSignalRep1K562Ctcf_327    to wgEncodeUtaChIPseqRawSignalRep1K562Ctcf   ;
rename table wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf_327 to wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf;
rename table wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc_327  to wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc ;
rename table wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf_327  to wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf ;
rename table wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc_327   to wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc  ;
rename table wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf_327   to wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf  ;
rename table wgEncodeUtaChIPseqRawSignalRep2K562Cmyc_327    to wgEncodeUtaChIPseqRawSignalRep2K562Cmyc   ;
rename table wgEncodeUtaChIPseqRawSignalRep2K562Ctcf_327    to wgEncodeUtaChIPseqRawSignalRep2K562Ctcf   ;
rename table wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf_327 to wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf;
rename table wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc_327   to wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc  ;
rename table wgEncodeUtaChIPseqRawSignalRep3K562Cmyc_327    to wgEncodeUtaChIPseqRawSignalRep3K562Cmyc   ;
rename table wgEncodeUtaChIPseqRawSignalRep3K562Ctcf_327    to wgEncodeUtaChIPseqRawSignalRep3K562Ctcf   ;

drop table wgEncodeUtaChIPseqRawSignalGm12878Input;
drop table wgEncodeUtaChIPseqRawSignalHelas3Input ;
drop table wgEncodeUtaChIPseqRawSignalHepg2Input  ;
drop table wgEncodeUtaChIPseqRawSignalK562Input   ;

rename table wgEncodeUtaChIPseqRawSignalGm12878Input_328 to wgEncodeUtaChIPseqRawSignalGm12878Input;
rename table wgEncodeUtaChIPseqRawSignalHelas3Input_328  to wgEncodeUtaChIPseqRawSignalHelas3Input ;
rename table wgEncodeUtaChIPseqRawSignalHepg2Input_328   to wgEncodeUtaChIPseqRawSignalHepg2Input  ;
rename table wgEncodeUtaChIPseqRawSignalK562Input_328    to wgEncodeUtaChIPseqRawSignalK562Input   ; 

cd /hive/groups/encode/dcc/pipeline/encpipeline_prod/325
mv wgEncodeDukeDNaseSeqRawSignalRep1Gm12878_325.wib wgEncodeDukeDNaseSeqRawSignalRep1Gm12878.wib
mv wgEncodeDukeDNaseSeqRawSignalRep1Helas3_325.wib  wgEncodeDukeDNaseSeqRawSignalRep1Helas3.wib
mv wgEncodeDukeDNaseSeqRawSignalRep1Hepg2_325.wib   wgEncodeDukeDNaseSeqRawSignalRep1Hepg2.wib
mv wgEncodeDukeDNaseSeqRawSignalRep1K562_325.wib    wgEncodeDukeDNaseSeqRawSignalRep1K562.wib
mv wgEncodeDukeDNaseSeqRawSignalRep2Gm12878_325.wib wgEncodeDukeDNaseSeqRawSignalRep2Gm12878.wib
mv wgEncodeDukeDNaseSeqRawSignalRep2Helas3_325.wib  wgEncodeDukeDNaseSeqRawSignalRep2Helas3.wib
mv wgEncodeDukeDNaseSeqRawSignalRep2Hepg2_325.wib   wgEncodeDukeDNaseSeqRawSignalRep2Hepg2.wib
mv wgEncodeDukeDNaseSeqRawSignalRep2K562_325.wib    wgEncodeDukeDNaseSeqRawSignalRep2K562.wib
mv wgEncodeDukeDNaseSeqRawSignalRep3Gm12878_325.wib wgEncodeDukeDNaseSeqRawSignalRep3Gm12878.wib
mv wgEncodeDukeDNaseSeqRawSignalRep3Helas3_325.wib  wgEncodeDukeDNaseSeqRawSignalRep3Helas3.wib
mv wgEncodeDukeDNaseSeqRawSignalRep3Hepg2_325.wib   wgEncodeDukeDNaseSeqRawSignalRep3Hepg2.wib
mv wgEncodeDukeDNaseSeqRawSignalRep3K562_325.wib    wgEncodeDukeDNaseSeqRawSignalRep3K562.wib

cd /gbdb/hg18/wib/ 
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep1Gm12878.wib  wgEncodeDukeDNaseSeqRawSignalRep1Gm12878.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep1Helas3.wib   wgEncodeDukeDNaseSeqRawSignalRep1Helas3.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep1Hepg2.wib    wgEncodeDukeDNaseSeqRawSignalRep1Hepg2.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep1K562.wib     wgEncodeDukeDNaseSeqRawSignalRep1K562.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep2Gm12878.wib  wgEncodeDukeDNaseSeqRawSignalRep2Gm12878.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep2Helas3.wib   wgEncodeDukeDNaseSeqRawSignalRep2Helas3.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep2Hepg2.wib    wgEncodeDukeDNaseSeqRawSignalRep2Hepg2.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep2K562.wib     wgEncodeDukeDNaseSeqRawSignalRep2K562.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep3Gm12878.wib  wgEncodeDukeDNaseSeqRawSignalRep3Gm12878.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep3Helas3.wib   wgEncodeDukeDNaseSeqRawSignalRep3Helas3.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep3Hepg2.wib    wgEncodeDukeDNaseSeqRawSignalRep3Hepg2.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/325/wgEncodeDukeDNaseSeqRawSignalRep3K562.wib     wgEncodeDukeDNaseSeqRawSignalRep3K562.wib

update wgEncodeDukeDNaseSeqRawSignalRep1Gm12878 set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep1Gm12878.wib";
update wgEncodeDukeDNaseSeqRawSignalRep1Helas3  set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep1Helas3.wib";
update wgEncodeDukeDNaseSeqRawSignalRep1Hepg2   set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep1Hepg2.wib";
update wgEncodeDukeDNaseSeqRawSignalRep1K562    set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep1K562.wib";
update wgEncodeDukeDNaseSeqRawSignalRep2Gm12878 set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep2Gm12878.wib";
update wgEncodeDukeDNaseSeqRawSignalRep2Helas3  set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep2Helas3.wib";
update wgEncodeDukeDNaseSeqRawSignalRep2Hepg2   set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep2Hepg2.wib";
update wgEncodeDukeDNaseSeqRawSignalRep2K562    set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep2K562.wib";
update wgEncodeDukeDNaseSeqRawSignalRep3Gm12878 set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep3Gm12878.wib";
update wgEncodeDukeDNaseSeqRawSignalRep3Helas3  set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep3Helas3.wib";
update wgEncodeDukeDNaseSeqRawSignalRep3Hepg2   set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep3Hepg2.wib";
update wgEncodeDukeDNaseSeqRawSignalRep3K562    set file = "/gbdb/hg18/wib/wgEncodeDukeDNaseSeqRawSignalRep3K562.wib";


cd /hive/groups/encode/dcc/pipeline/encpipeline_prod/326
mv wgEncodeUncFAIREseqRawSignalRep1Gm12878_326.wib wgEncodeUncFAIREseqRawSignalRep1Gm12878.wib
mv wgEncodeUncFAIREseqRawSignalRep1Helas3_326.wib  wgEncodeUncFAIREseqRawSignalRep1Helas3.wib
mv wgEncodeUncFAIREseqRawSignalRep1Hepg2_326.wib   wgEncodeUncFAIREseqRawSignalRep1Hepg2.wib
mv wgEncodeUncFAIREseqRawSignalRep1K562_326.wib    wgEncodeUncFAIREseqRawSignalRep1K562.wib
mv wgEncodeUncFAIREseqRawSignalRep2Gm12878_326.wib wgEncodeUncFAIREseqRawSignalRep2Gm12878.wib
mv wgEncodeUncFAIREseqRawSignalRep2Helas3_326.wib  wgEncodeUncFAIREseqRawSignalRep2Helas3.wib
mv wgEncodeUncFAIREseqRawSignalRep2Hepg2_326.wib   wgEncodeUncFAIREseqRawSignalRep2Hepg2.wib
mv wgEncodeUncFAIREseqRawSignalRep2K562_326.wib    wgEncodeUncFAIREseqRawSignalRep2K562.wib
mv wgEncodeUncFAIREseqRawSignalRep3Gm12878_326.wib wgEncodeUncFAIREseqRawSignalRep3Gm12878.wib
mv wgEncodeUncFAIREseqRawSignalRep3Helas3_326.wib  wgEncodeUncFAIREseqRawSignalRep3Helas3.wib
mv wgEncodeUncFAIREseqRawSignalRep3Hepg2_326.wib   wgEncodeUncFAIREseqRawSignalRep3Hepg2.wib
mv wgEncodeUncFAIREseqRawSignalRep3K562_326.wib    wgEncodeUncFAIREseqRawSignalRep3K562.wib

cd /gbdb/hg18/wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep1Gm12878.wib wgEncodeUncFAIREseqRawSignalRep1Gm12878.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep1Helas3.wib  wgEncodeUncFAIREseqRawSignalRep1Helas3.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep1Hepg2.wib   wgEncodeUncFAIREseqRawSignalRep1Hepg2.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep1K562.wib    wgEncodeUncFAIREseqRawSignalRep1K562.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep2Gm12878.wib wgEncodeUncFAIREseqRawSignalRep2Gm12878.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep2Helas3.wib  wgEncodeUncFAIREseqRawSignalRep2Helas3.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep2Hepg2.wib   wgEncodeUncFAIREseqRawSignalRep2Hepg2.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep2K562.wib    wgEncodeUncFAIREseqRawSignalRep2K562.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep3Gm12878.wib wgEncodeUncFAIREseqRawSignalRep3Gm12878.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep3Helas3.wib  wgEncodeUncFAIREseqRawSignalRep3Helas3.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep3Hepg2.wib   wgEncodeUncFAIREseqRawSignalRep3Hepg2.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/326/wgEncodeUncFAIREseqRawSignalRep3K562.wib    wgEncodeUncFAIREseqRawSignalRep3K562.wib

update wgEncodeUncFAIREseqRawSignalRep1Gm12878 set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep1Gm12878.wib";
update wgEncodeUncFAIREseqRawSignalRep1Helas3  set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep1Helas3.wib";
update wgEncodeUncFAIREseqRawSignalRep1Hepg2   set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep1Hepg2.wib";
update wgEncodeUncFAIREseqRawSignalRep1K562    set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep1K562.wib";
update wgEncodeUncFAIREseqRawSignalRep2Gm12878 set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep2Gm12878.wib";
update wgEncodeUncFAIREseqRawSignalRep2Helas3  set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep2Helas3.wib";
update wgEncodeUncFAIREseqRawSignalRep2Hepg2   set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep2Hepg2.wib";
update wgEncodeUncFAIREseqRawSignalRep2K562    set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep2K562.wib";
update wgEncodeUncFAIREseqRawSignalRep3Gm12878 set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep3Gm12878.wib";
update wgEncodeUncFAIREseqRawSignalRep3Helas3  set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep3Helas3.wib";
update wgEncodeUncFAIREseqRawSignalRep3Hepg2   set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep3Hepg2.wib";
update wgEncodeUncFAIREseqRawSignalRep3K562    set file = "/gbdb/hg18/wib/wgEncodeUncFAIREseqRawSignalRep3K562.wib";


cd /hive/groups/encode/dcc/pipeline/encpipeline_prod/327
mv wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf_327.wib wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc_327.wib  wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc.wib
mv wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf_327.wib  wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc_327.wib   wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc.wib
mv wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf_327.wib   wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep1K562Cmyc_327.wib    wgEncodeUtaChIPseqRawSignalRep1K562Cmyc.wib
mv wgEncodeUtaChIPseqRawSignalRep1K562Ctcf_327.wib    wgEncodeUtaChIPseqRawSignalRep1K562Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf_327.wib wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc_327.wib  wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc.wib
mv wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf_327.wib  wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc_327.wib   wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc.wib
mv wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf_327.wib   wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep2K562Cmyc_327.wib    wgEncodeUtaChIPseqRawSignalRep2K562Cmyc.wib
mv wgEncodeUtaChIPseqRawSignalRep2K562Ctcf_327.wib    wgEncodeUtaChIPseqRawSignalRep2K562Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf_327.wib wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf.wib
mv wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc_327.wib   wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc.wib
mv wgEncodeUtaChIPseqRawSignalRep3K562Cmyc_327.wib    wgEncodeUtaChIPseqRawSignalRep3K562Cmyc.wib
mv wgEncodeUtaChIPseqRawSignalRep3K562Ctcf_327.wib    wgEncodeUtaChIPseqRawSignalRep3K562Ctcf.wib

cd /gbdb/hg18/wib/ 
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf.wib wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc.wib  wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf.wib  wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc.wib   wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf.wib   wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep1K562Cmyc.wib    wgEncodeUtaChIPseqRawSignalRep1K562Cmyc.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep1K562Ctcf.wib    wgEncodeUtaChIPseqRawSignalRep1K562Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf.wib wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc.wib  wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf.wib  wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc.wib   wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf.wib   wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep2K562Cmyc.wib    wgEncodeUtaChIPseqRawSignalRep2K562Cmyc.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep2K562Ctcf.wib    wgEncodeUtaChIPseqRawSignalRep2K562Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf.wib wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc.wib   wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep3K562Cmyc.wib    wgEncodeUtaChIPseqRawSignalRep3K562Cmyc.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/327/wgEncodeUtaChIPseqRawSignalRep3K562Ctcf.wib    wgEncodeUtaChIPseqRawSignalRep3K562Ctcf.wib

update wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep1Gm12878Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc  set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep1Helas3Cmyc.wib";
update wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf  set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep1Helas3Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc   set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep1Hepg2Cmyc.wib";
update wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf   set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep1Hepg2Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep1K562Cmyc    set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep1K562Cmyc.wib";
update wgEncodeUtaChIPseqRawSignalRep1K562Ctcf    set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep1K562Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep2Gm12878Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc  set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep2Helas3Cmyc.wib";
update wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf  set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep2Helas3Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc   set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep2Hepg2Cmyc.wib";
update wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf   set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep2Hepg2Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep2K562Cmyc    set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep2K562Cmyc.wib";
update wgEncodeUtaChIPseqRawSignalRep2K562Ctcf    set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep2K562Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep3Gm12878Ctcf.wib";
update wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc   set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep3Hepg2Cmyc.wib";
update wgEncodeUtaChIPseqRawSignalRep3K562Cmyc    set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep3K562Cmyc.wib";
update wgEncodeUtaChIPseqRawSignalRep3K562Ctcf    set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalRep3K562Ctcf.wib";
 

cd /hive/groups/encode/dcc/pipeline/encpipeline_prod/328
mv wgEncodeUtaChIPseqRawSignalGm12878Input_328.wib wgEncodeUtaChIPseqRawSignalGm12878Input.wib
mv wgEncodeUtaChIPseqRawSignalHelas3Input_328.wib  wgEncodeUtaChIPseqRawSignalHelas3Input.wib
mv wgEncodeUtaChIPseqRawSignalHepg2Input_328.wib   wgEncodeUtaChIPseqRawSignalHepg2Input.wib
mv wgEncodeUtaChIPseqRawSignalK562Input_328.wib    wgEncodeUtaChIPseqRawSignalK562Input.wib

cd /gbdb/hg18/wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/328/wgEncodeUtaChIPseqRawSignalGm12878Input.wib wgEncodeUtaChIPseqRawSignalGm12878Input.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/328/wgEncodeUtaChIPseqRawSignalHelas3Input.wib  wgEncodeUtaChIPseqRawSignalHelas3Input.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/328/wgEncodeUtaChIPseqRawSignalHepg2Input.wib   wgEncodeUtaChIPseqRawSignalHepg2Input.wib
ln -sf /hive/groups/encode/dcc/pipeline/encpipeline_prod/328/wgEncodeUtaChIPseqRawSignalK562Input.wib    wgEncodeUtaChIPseqRawSignalK562Input.wib

update wgEncodeUtaChIPseqRawSignalGm12878Input set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalGm12878Input.wib";
update wgEncodeUtaChIPseqRawSignalHelas3Input  set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalHelas3Input.wib"; 
update wgEncodeUtaChIPseqRawSignalHepg2Input   set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalHepg2Input.wib";  
update wgEncodeUtaChIPseqRawSignalK562Input    set file = "/gbdb/hg18/wib/wgEncodeUtaChIPseqRawSignalK562Input.wib";   

Load FAIRE Hela-S3 peaks which are missing 2009-05-22
=====================================================
# validation error on 336 because table in trackDb
delete from trackDb where tableName like "wgEncodeUncFAIREseqPeaksHelas3";        
# validation error because of zero length peak: Ask Terry.

/cluster/data/encode/pipeline/bin/encodeStatus.pl 336 displayed
        
Generate RawSignal files for download 2009-5-28
===============================================
from pip
grep RawSignal 325/out/load.ra | grep auto >> 325/out/mkRawSigsFiles.sh 
grep RawSignal 325/out/load.ra | grep wgEncode >> 325/out/mkRawSigsFiles.sh 
...
Edit and then run 325/out/mkRawSigsFiles.sh
placing *.wig.gz into downloads/wgEncodeChromatinMap/raw
cd downloads/wgEncodeChromatinMap/raw
cp ../preamble.html
cp ../fileDb.ra
edit preamble.html to note the subdirectory only contains Raw Signals
encodeDownloadsPage.pl index.html

Pushed into QA 2009-06-02
=========================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 336 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl  31 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl  34 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 109 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 112 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 113 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 116 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 117 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 127 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 131 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 228 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 231 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 234 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 235 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 244 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 245 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 258 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 272 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 274 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 275 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 278 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 280 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 281 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 282 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 283 reviewing
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 285 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 286 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 287 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 325 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 326 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 327 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 328 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 336 reviewing

Pushed Mapability into QA 2009-06-15
====================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 104 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 344 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 345 approved
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New submissions 2009-09-01-07
==========================
select id,name,status, user_id from projects where user_id = 17 and status = "loaded";
+-----+-----------------------------------+--------+---------+
| id  | name                              | status | user_id |
+-----+-----------------------------------+--------+---------+
| 461 | DukeDnaseSeq GM12878 20090901     | loaded |      17 | 
| 468 | UTA CTCF GM12878 20090903         | loaded |      17 | 
| 471 | UNC FAIRE-Seq GM12878 20090906    | loaded |      17 | 
| 472 | UTA c-Myc GM12878 20090906        | loaded |      17 | 
| 482 | UTA ChIP-Seq c-Myc K562 20090906  | loaded |      17 | 
| 480 | Duke DNase-Seq K562 20090906      | loaded |      17 | 
| 481 | UTA ChIP-Seq CTCF K562 20090906   | loaded |      17 | 
| 483 | UNC FAIRE-Seq K562 20090906       | loaded |      17 | 
| 493 | UTA ChIP-Seq CTCF HelaS3 20090907 | loaded |      17 | 
| 494 | UNC FAIRE-Seq HelaS3 20090907     | loaded |      17 | 
| 495 | Duke DNase-Seq HelaS3 20090907    | loaded |      17 | 
+-----+-----------------------------------+--------+---------+
After some DAF manipulation and training Terry to new methods, all submitted fine.
I did some massaging if the trackDb and fileDb.ra recs.

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2009-10-02 Data trickling which is not quite part of the freeze
===============================================================
| 544 | DNCT UTA Input HUVEC 20090923                 | loaded        | 
| 545 | DNCT Duke DNaseHS HUVEC 20090924              | loaded        | 
| 546 | DNCT UNC FAIRE-Seq HUVEC 20090924             | loaded        | 
| 548 | DNCT UTA CTCF HUVEC 20090924                  | loaded        | 
| 552 | DNCT UTA PolII HUVEC 20090924                 | loaded        | 
| 555 | DNCT UTA CTCF HepG2 20090928                  | loaded        | 
| 556 | DNCT Duke DNaseHS HepG2 20090928              | loaded        | 
| 557 | DNCT UNC FAIRE-Seq HepG2 20090928             | loaded        | 
| 589 | DNCT UTA PolII HepG2 20090929                 | loaded        | 
| 588 | DNCT UTA PolII K562 20090929                  | loaded        | 
| 593 | DNCT UTA c-Myc HepG2 20090929                 | loaded        | 
| 594 | DNCT Duke DNaseHS Keratinocyte 20090929       | loaded        | 
| 624 | DNCT UTA CTCF NHEK 20090929                   | loaded        | 
| 628 | DNCT Duke DNaseHS H1_hESC 20090930            | loaded        | 
| 629 | DNCT UNC FAIRE-Seq H1-hESC 20090930           | loaded        | 
| 630 | DNCT UNC FAIRE-Seq NHEK 20090930              | loaded        | 
| 635 | DNCT UTA c-Myc HUVEC 20091001                 | loaded        | 
| 636 | DNCT UTA CTCF H1_hESC 20091001                | loaded        | 
| 638 | DNCT UTA CTCF GM12892 20091002                | loaded        | 
| 639 | DNCT UNC FAIRE-Seq HelaS3 20091002            | loaded        | 
| 640 | DNCT UNC FAIRE-Seq K562 20091002              | loaded        | 
| 641 | DNCT UTA PolII H1_hESC 20091002               | loaded        | 

Tracy Ballinger has been working tirelessly to put the trackDb.wgEncode.ra and downloads dir into shape.

2009-10-12 Bring the trackDb.wgEncode/ra up-to-date
===================================================
make alpha DBS=hg18
cd {downloadsDir}
### First prepare old release1 directory:
mkdir release1
# save source of the RR index.html
mv ../old/wgEncodeUtaChIPseqRawDataRep1Gm12878Ctcf.fastq.gz .
mv ../old/wgEncodeUtaChIPseqRawDataRep2Gm12878Ctcf.fastq.gz .
mv ../old/wgEncodeUtaChIPseqRawDataRep3Gm12878Ctcf.fastq.gz .
mv ../old/wgEncodeUtaChIPseqPeaksGm12878Ctcf.narrowPeak.gz  .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep1Gm12878Ctcf.tagAlign.gz    .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep2Gm12878Ctcf.tagAlign.gz    .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep3Gm12878Ctcf.tagAlign.gz    .
mv ../old/wgEncodeUtaChIPseqBaseOverlapSignalGm12878Ctcf.wig.gz      .
mv ../old/wgEncodeUtaChIPseqSignalGm12878Ctcf.wig.gz                 .
ln ../wgEncodeUtaustinChIPseqRawDataGm12878Input.fastq.gz        .
ln ../wgEncodeUtaustinChIPseqAlignmentsGm12878Input.tagAlign.gz  .
ln ../wgEncodeUtaustinChIPseqSignalGm12878Input.wig.gz           .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep1Gm12878.fastq.gz            .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep2Gm12878.fastq.gz            .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep3Gm12878.fastq.gz            .
mv ../old/wgEncodeDukeDNaseSeqPeaksGm12878.narrowPeak.gz             .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep1Gm12878.tagAlign.gz      .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep2Gm12878.tagAlign.gz      .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep3Gm12878.tagAlign.gz      .
mv ../old/wgEncodeDukeDNaseSeqBaseOverlapSignalGm12878.wig.gz        .
mv ../old/wgEncodeDukeDNaseSeqSignalGm12878.wig.gz                   .
mv ../old/wgEncodeUncFAIREseqRawDataRep1Gm12878.fastq.gz             .
mv ../old/wgEncodeUncFAIREseqRawDataRep2Gm12878.fastq.gz             .
mv ../old/wgEncodeUncFAIREseqRawDataRep3Gm12878.fastq.gz             .
mv ../old/wgEncodeUncFAIREseqPeaksGm12878.narrowPeak.gz              .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep1Gm12878.tagAlign.gz       .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep2Gm12878.tagAlign.gz       .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep3Gm12878.tagAlign.gz       .
mv ../old/wgEncodeUncFAIREseqBaseOverlapSignalGm12878.wig.gz         .
mv ../old/wgEncodeUncFAIREseqSignalGm12878.wig.gz                    .
mv ../old/wgEncodeUtaChIPseqRawDataRep1Helas3Ctcf.fastq.gz           .
mv ../old/wgEncodeUtaChIPseqRawDataRep2Helas3Ctcf.fastq.gz           .
mv ../old/wgEncodeUtaChIPseqPeaksHelas3Ctcf.narrowPeak.gz            .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep1Helas3Ctcf.tagAlign.gz     .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep2Helas3Ctcf.tagAlign.gz     .
mv ../old/wgEncodeUtaChIPseqBaseOverlapSignalHelas3Ctcf.wig.gz       .
mv ../old/wgEncodeUtaChIPseqSignalHelas3Ctcf.wig.gz                  .
ln ../wgEncodeUtaustinChIPseqRawDataHelas3Input.fastq.gz         .
ln ../wgEncodeUtaustinChIPseqAlignmentsHelas3Input.tagAlign.gz   .
ln ../wgEncodeUtaustinChIPseqSignalHelas3Input.wig.gz            .
ln ../wgEncodeUtaChIPseqRawDataRep1Helas3Cmyc.fastq.gz           .
ln ../wgEncodeUtaChIPseqRawDataRep2Helas3Cmyc.fastq.gz           .
ln ../wgEncodeUtaChIPseqPeaksHelas3Cmyc.narrowPeak.gz            .
ln ../wgEncodeUtaChIPseqAlignmentsRep1Helas3Cmyc.tagAlign.gz     .
ln ../wgEncodeUtaChIPseqAlignmentsRep2Helas3Cmyc.tagAlign.gz     .
ln ../wgEncodeUtaChIPseqBaseOverlapSignalHelas3Cmyc.wig.gz       .
ln ../wgEncodeUtaChIPseqSignalHelas3Cmyc.wig.gz                  .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep1Helas3.fastq.gz             .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep2Helas3.fastq.gz             .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep3Helas3.fastq.gz             .
mv ../old/wgEncodeDukeDNaseSeqPeaksHelas3.narrowPeak.gz              .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep1Helas3.tagAlign.gz       .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep2Helas3.tagAlign.gz       .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep3Helas3.tagAlign.gz       .
mv ../old/wgEncodeDukeDNaseSeqBaseOverlapSignalHelas3.wig.gz         .
mv ../old/wgEncodeDukeDNaseSeqSignalHelas3.wig.gz                    .
mv ../old/wgEncodeUncFAIREseqRawDataRep1Helas3.fastq.gz              .
mv ../old/wgEncodeUncFAIREseqRawDataRep2Helas3.fastq.gz              .
mv ../old/wgEncodeUncFAIREseqRawDataRep3Helas3.fastq.gz              .
mv ../old/wgEncodeUncFAIREseqPeaksHelas3.narrowPeak.gz               .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep1Helas3.tagAlign.gz        .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep2Helas3.tagAlign.gz        .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep3Helas3.tagAlign.gz        .
mv ../old/wgEncodeUncFAIREseqBaseOverlapSignalHelas3.wig.gz          .
mv ../old/wgEncodeUncFAIREseqSignalHelas3.wig.gz                     .
mv ../old/wgEncodeUtaChIPseqRawDataRep1Hepg2Ctcf.fastq.gz            .
mv ../old/wgEncodeUtaChIPseqRawDataRep2Hepg2Ctcf.fastq.gz            .
mv ../old/wgEncodeUtaChIPseqPeaksHepg2Ctcf.narrowPeak.gz             .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep1Hepg2Ctcf.tagAlign.gz      .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep2Hepg2Ctcf.tagAlign.gz      .
mv ../old/wgEncodeUtaChIPseqBaseOverlapSignalHepg2Ctcf.wig.gz        .
mv ../old/wgEncodeUtaChIPseqSignalHepg2Ctcf.wig.gz                   .
ln ../wgEncodeUtaustinChIPseqRawDataHepg2Input.fastq.gz          .
ln ../wgEncodeUtaustinChIPseqAlignmentsHepg2Input.tagAlign.gz    .
ln ../wgEncodeUtaustinChIPseqSignalHepg2Input.wig.gz             .
mv ../old/wgEncodeUtaChIPseqRawDataRep1Hepg2Cmyc.fastq.gz            .
mv ../old/wgEncodeUtaChIPseqRawDataRep2Hepg2Cmyc.fastq.gz            .
mv ../old/wgEncodeUtaChIPseqRawDataRep3Hepg2Cmyc.fastq.gz            .
mv ../old/wgEncodeUtaChIPseqPeaksHepg2Cmyc.narrowPeak.gz             .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep1Hepg2Cmyc.tagAlign.gz      .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep2Hepg2Cmyc.tagAlign.gz      .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep3Hepg2Cmyc.tagAlign.gz      .
mv ../old/wgEncodeUtaChIPseqBaseOverlapSignalHepg2Cmyc.wig.gz        .
mv ../old/wgEncodeUtaChIPseqSignalHepg2Cmyc.wig.gz                   .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep1Hepg2.fastq.gz              .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep2Hepg2.fastq.gz              .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep3Hepg2.fastq.gz              .
mv ../old/wgEncodeDukeDNaseSeqPeaksHepg2.narrowPeak.gz               .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep1Hepg2.tagAlign.gz        .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep2Hepg2.tagAlign.gz        .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep3Hepg2.tagAlign.gz        .
mv ../old/wgEncodeDukeDNaseSeqBaseOverlapSignalHepg2.wig.gz          .
mv ../old/wgEncodeDukeDNaseSeqSignalHepg2.wig.gz                     .
mv ../old/wgEncodeUncFAIREseqRawDataRep1Hepg2.fastq.gz               .
mv ../old/wgEncodeUncFAIREseqRawDataRep2Hepg2.fastq.gz               .
mv ../old/wgEncodeUncFAIREseqRawDataRep3Hepg2.fastq.gz               .
mv ../old/wgEncodeUncFAIREseqPeaksHepg2.narrowPeak.gz                .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep1Hepg2.tagAlign.gz         .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep2Hepg2.tagAlign.gz         .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep3Hepg2.tagAlign.gz         .
mv ../old/wgEncodeUncFAIREseqBaseOverlapSignalHepg2.wig.gz           .
mv ../old/wgEncodeUncFAIREseqSignalHepg2.wig.gz                      .
mv ../old/wgEncodeUtaChIPseqRawDataRep1K562Ctcf.fastq.gz             .
mv ../old/wgEncodeUtaChIPseqRawDataRep2K562Ctcf.fastq.gz             .
mv ../old/wgEncodeUtaChIPseqRawDataRep3K562Ctcf.fastq.gz             .
mv ../old/wgEncodeUtaChIPseqPeaksK562Ctcf.narrowPeak.gz              .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep1K562Ctcf.tagAlign.gz       .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep2K562Ctcf.tagAlign.gz       .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep3K562Ctcf.tagAlign.gz       .
mv ../old/wgEncodeUtaChIPseqBaseOverlapSignalK562Ctcf.wig.gz         .
mv ../old/wgEncodeUtaChIPseqSignalK562Ctcf.wig.gz                    .
ln ../wgEncodeUtaustinChIPseqRawDataK562Input.fastq.gz           .
ln ../wgEncodeUtaustinChIPseqAlignmentsK562Input.tagAlign.gz     .
ln ../wgEncodeUtaustinChIPseqSignalK562Input.wig.gz              .
mv ../old/wgEncodeUtaChIPseqRawDataRep1K562Cmyc.fastq.gz             .
mv ../old/wgEncodeUtaChIPseqRawDataRep2K562Cmyc.fastq.gz             .
mv ../old/wgEncodeUtaChIPseqRawDataRep3K562Cmyc.fastq.gz             .
mv ../old/wgEncodeUtaChIPseqPeaksK562Cmyc.narrowPeak.gz              .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep1K562Cmyc.tagAlign.gz       .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep2K562Cmyc.tagAlign.gz       .
mv ../old/wgEncodeUtaChIPseqAlignmentsRep3K562Cmyc.tagAlign.gz       .
mv ../old/wgEncodeUtaChIPseqBaseOverlapSignalK562Cmyc.wig.gz         .
mv ../old/wgEncodeUtaChIPseqSignalK562Cmyc.wig.gz                    .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep1K562.fastq.gz               .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep2K562.fastq.gz               .
mv ../old/wgEncodeDukeDNaseSeqRawDataRep3K562.fastq.gz               .
mv ../old/wgEncodeDukeDNaseSeqPeaksK562.narrowPeak.gz                .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep1K562.tagAlign.gz         .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep2K562.tagAlign.gz         .
mv ../old/wgEncodeDukeDNaseSeqAlignmentsRep3K562.tagAlign.gz         .
mv ../old/wgEncodeDukeDNaseSeqBaseOverlapSignalK562.wig.gz           .
mv ../old/wgEncodeDukeDNaseSeqSignalK562.wig.gz                      .
mv ../old/wgEncodeUncFAIREseqRawDataRep1K562.fastq.gz                .
mv ../old/wgEncodeUncFAIREseqRawDataRep2K562.fastq.gz                .
mv ../old/wgEncodeUncFAIREseqRawDataRep3K562.fastq.gz                .
mv ../old/wgEncodeUncFAIREseqPeaksK562.narrowPeak.gz                 .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep1K562.tagAlign.gz          .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep2K562.tagAlign.gz          .
mv ../old/wgEncodeUncFAIREseqAlignmentsRep3K562.tagAlign.gz          .
mv ../old/wgEncodeUncFAIREseqBaseOverlapSignalK562.wig.gz            .
mv ../old/wgEncodeUncFAIREseqSignalK562.wig.gz                       .

### Now move in all of the newly submitted files
cd ..
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep1Gm12891.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep1Gm12892.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep1Gm19238.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep1Gm19239.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep1Gm19240.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep1H1hesc.tagAlign.gz    .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep2Gm12891.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep2Gm12892.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep2Gm19238.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep2Gm19239.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep2Gm19240.tagAlign.gz   .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqAlignmentsRep2H1hesc.tagAlign.gz    .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqBaseOverlapSignalH1hesc.wig.gz      .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12891.wig.gz .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12892.wig.gz .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19238.wig.gz .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19239.wig.gz .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19240.wig.gz .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqPeaksH1hesc.narrowPeak.gz           .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqPeaksRep1Gm12891.narrowPeak.gz      .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqPeaksRep1Gm12892.narrowPeak.gz      .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqPeaksRep1Gm19238.narrowPeak.gz      .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqPeaksRep1Gm19239.narrowPeak.gz      .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqPeaksRep1Gm19240.narrowPeak.gz      .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep1Gm12891.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep1Gm12892.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep1Gm19238.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep1Gm19239.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep1Gm19240.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep1H1hesc.fastq.gz          .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep2Gm12891.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep2Gm12892.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep2Gm19238.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep2Gm19239.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep2Gm19240.fastq.gz         .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqRawDataRep2H1hesc.fastq.gz          .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqSignalH1hesc.wig.gz                 .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqSignalRep1Gm12891.wig.gz            .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqSignalRep1Gm12892.wig.gz            .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqSignalRep1Gm19238.wig.gz            .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqSignalRep1Gm19239.wig.gz            .
mv -i ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqSignalRep1Gm19240.wig.gz            .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqAlignmentsRep1H1hesc.tagAlign.gz      .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqAlignmentsRep1Helas3V2.tagAlign.gz    .  y
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqAlignmentsRep1K562V2.tagAlign.gz      .  y
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqAlignmentsRep1Nhek.tagAlign.gz        .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqAlignmentsRep2H1hesc.tagAlign.gz      .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqAlignmentsRep2Helas3V2.tagAlign.gz    .  y
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqAlignmentsRep2K562V2.tagAlign.gz      .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqAlignmentsRep2Nhek.tagAlign.gz        .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqBaseOverlapSignalH1hesc.wig.gz        .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqBaseOverlapSignalRep1Helas3V2.wig.gz  .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqBaseOverlapSignalRep1K562V2.wig.gz    .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqBaseOverlapSignalRep1Nhek.wig.gz      .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqPeaksH1hesc.narrowPeak.gz             .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqPeaksRep1Helas3V2.narrowPeak.gz       .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqPeaksRep1K562V2.narrowPeak.gz         .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqPeaksRep1Nhek.narrowPeak.gz           .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqRawDataRep1H1hesc.fastq.gz            .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqRawDataRep1Helas3V2.fastq.gz          .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqRawDataRep1K562V2.fastq.gz            .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqRawDataRep1Nhek.fastq.gz              .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqRawDataRep2H1hesc.fastq.gz            .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqRawDataRep2Helas3V2.fastq.gz          .  y
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqRawDataRep2K562V2.fastq.gz            .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqRawDataRep2Nhek.fastq.gz              .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqSignalH1hesc.wig.gz                   .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqSignalRep1Helas3V2.wig.gz             .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqSignalRep1K562V2.wig.gz               .
mv -i ../wgEncodeUncFAIREseq/wgEncodeUncFAIREseqSignalRep1Nhek.wig.gz                 .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsH1hescCtcf.tagAlign.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsH1hescPol2.tagAlign.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsHuvecCmyc.tagAlign.gz         .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep1Gm12891Ctcf.tagAlign.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep1Gm12892Ctcf.tagAlign.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep1Gm19238Ctcf.tagAlign.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep1Gm19239Ctcf.tagAlign.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep1Gm19240Ctcf.tagAlign.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep1Helas3CmycV2.tagAlign.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep1NhekCtcf.tagAlign.gz       .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep2Gm12891Ctcf.tagAlign.gz    .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep2Gm12892Ctcf.tagAlign.gz    .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep2Gm19238Ctcf.tagAlign.gz    .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep2Gm19239Ctcf.tagAlign.gz    .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep2Gm19240Ctcf.tagAlign.gz    .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep2Helas3CmycV2.tagAlign.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqAlignmentsRep2NhekCtcf.tagAlign.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalH1hescCtcf.wig.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalH1hescPol2.wig.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalHuvecCmyc.wig.gz         .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalNhekCtcf.wig.gz          .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12891Ctcf.wig.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12892Ctcf.wig.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19238Ctcf.wig.gz   .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19239Ctcf.wig.gz  .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19240Ctcf.wig.gz  .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalRep1Helas3CmycV2.wig.gz .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksH1hescCtcf.narrowPeak.gz            .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksH1hescPol2.narrowPeak.gz            .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksHuvecCmyc.narrowPeak.gz             .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksNhekCtcf.narrowPeak.gz              .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksRep1Gm12891Ctcf.narrowPeak.gz       .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksRep1Gm12892Ctcf.narrowPeak.gz      .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksRep1Gm19238Ctcf.narrowPeak.gz      .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksRep1Gm19239Ctcf.narrowPeak.gz      .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksRep1Gm19240Ctcf.narrowPeak.gz      .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqPeaksRep1Helas3CmycV2.narrowPeak.gz     .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataH1hescCtcf.fastq.gz              .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataH1hescPol2.fastq.gz              .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataHuvecCmyc.fastq.gz               .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep1Gm12891Ctcf.fastq.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep1Gm12892Ctcf.fastq.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep1Gm19238Ctcf.fastq.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep1Gm19239Ctcf.fastq.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep1Gm19240Ctcf.fastq.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep1Helas3CmycV2.fastq.gz       .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep1NhekCtcf.fastq.gz           .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep2Gm12891Ctcf.fastq.gz        .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep2Gm12892Ctcf.fastq.gz       .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep2Gm19238Ctcf.fastq.gz       .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep2Gm19239Ctcf.fastq.gz       .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep2Gm19240Ctcf.fastq.gz       .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep2Helas3CmycV2.fastq.gz      .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqRawDataRep2NhekCtcf.fastq.gz          .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalH1hescCtcf.wig.gz               .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalH1hescPol2.wig.gz               .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalHuvecCmyc.wig.gz               .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalNhekCtcf.wig.gz                .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalRep1Gm12891Ctcf.wig.gz         .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalRep1Gm12892Ctcf.wig.gz         .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalRep1Gm19238Ctcf.wig.gz         .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalRep1Gm19239Ctcf.wig.gz         .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalRep1Gm19240Ctcf.wig.gz         .
mv -i ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqSignalRep1Helas3CmycV2.wig.gz        .

### Next, get the download only file metadata set properly
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/544/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/545/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/546/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/548/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/552/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/555/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/556/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/557/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/589/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/588/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/593/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/594/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/624/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/628/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/629/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/630/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/635/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/636/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/638/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/639/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/640/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/641/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/642/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/643/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/644/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/645/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/646/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/647/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/648/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/650/out/fileDb.ra | grep parentTable >> tmp.txt

grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/649/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/651/out/fileDb.ra | grep parentTable >> tmp.txt

# edit tmp.txt
cp fileDb.ra fileDb.ra.2009-10-12
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html

# fix some problems 
# 1) noticed 649 and 651 had been left off the list
# 2) superceding actions left behind files when names did not conflict! 
mkdir superceded
# Resubmit V2 with (Rep1 in name!)
mv wgEncodeUncFAIREseqBaseOverlapSignalHelas3V2.wig.gz  superceded/
mv wgEncodeUncFAIREseqSignalHelas3V2.wig.gz             superceded/

# Submit V2, but V1 was not released yet
mv wgEncodeUtaChIPseqBaseOverlapSignalHelas3Cmyc.wig.gz superceded/
mv wgEncodeUtaChIPseqPeaksHelas3Cmyc.narrowPeak.gz      superceded/
mv wgEncodeUtaChIPseqSignalHelas3Cmyc.wig.gz            superceded/
  
# Resubmit V2 with (Rep1 in name!)
mv wgEncodeUncFAIREseqBaseOverlapSignalK562V2.wig.gz superceded/
mv wgEncodeUncFAIREseqSignalK562V2.wig.gz            superceded/

/cluster/data/encode/pipeline/bin/encodeStatus.pl 544 displayed
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 651 displayed

2009-10-14 One more
===================
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/686/out/fileDb.ra | grep parentTable >> tmp.txt
edit tmp.txt
cp fileDb.ra fileDb.ra.2009-10-14
cat tmp.txt >> fileDb..ra
encodeDownloadsPage.pl index.html
/cluster/data/encode/pipeline/bin/encodeStatus.pl 686 displayed

2009-10-23 Get ready for release 2
==================================
# edit wgEncodeChromatinMap.html to add release notes provided by Terry Furey
# edit metadata in trackDb to give version reasons

#Filter ranges:
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksGm12878     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksGm12878V2   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksH1hesc      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksHelas3      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksHelas3V2    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksHepg2       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksHepg2V2     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksHuvec       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksK562        ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksK562V2      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksNhek        ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksRep1Gm12891 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksRep1Gm12892 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksRep1Gm19238 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksRep1Gm19239 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeDukeDNaseSeqPeaksRep1Gm19240 ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksGm12878Cmyc     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksGm12878Ctcf     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksGm12878CtcfV2   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksH1hescCtcf      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksH1hescPol2      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHelas3Cmyc      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHelas3Ctcf      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHelas3CtcfV2    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHepg2Cmyc       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHepg2CmycV2     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHepg2Ctcf       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHepg2CtcfV2     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHepg2Pol2       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHuvecCmyc       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHuvecCtcf       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksHuvecPol2       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksK562Cmyc        ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksK562CmycV2      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksK562Ctcf        ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksK562CtcfV2      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksK562Pol2        ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksNhekCtcf        ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksRep1Gm12891Ctcf ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksRep1Gm12892Ctcf ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksRep1Gm19238Ctcf ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksRep1Gm19239Ctcf ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksRep1Gm19240Ctcf ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUtaChIPseqPeaksRep1Helas3CmycV2;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksGm12878     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksGm12878V2   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksH1hesc      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksHelas3      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksHelas3V2    ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksHepg2       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksHepg2V2     ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksHuvec       ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksK562        ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksK562V2      ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksPanislets   ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksRep1Helas3V2;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksRep1K562V2  ;
select min(score),max(score),min(signalValue),max(signalValue),min(pValue),max(pValue),min(qValue),max(qValue) from wgEncodeUncFAIREseqPeaksRep1Nhek    ;
# Result score 100:1000, signalValue 0:16 (but too variable to be useful) pValue 0:100, qValue -1:-1

# thus don't change filterBy settings in trackDb
# check in trackDb.wgEncode.ra, wgEncodeChomatinMap.html
make alpha DBS=hg18

# updating versioning info in downloads index.html
cd {downlodsDir}
cp fileDb.ra fileDb.ra.2009-10-23
grep parent fileDb.tmp.ra | sort | uniq > fileDb.ra
grep V2 fileDb.ra | sort | uniq > fileV2.ra
grep -v V2 fileDb.ra | sort | uniq > fileNV2.ra
# edit fileV2.ra
# do some massaging for duplicate lines or missing data
cp fileNV2.ra fileDb.ra
cat fileV2.ra >> fileDb.ra
encodeDownloadsPage.pl index.html 

# something missing
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/686/out/fileDb.ra | grep parentTable >> tmp.txt
cat tmp.txt >> fileDb.ra
sort < fileDb.ra > fileDbS.ra
rm fileDb.ra
mv fileDbS.ra fileDb.ra 
encodeDownloadsPage.pl index.html 

# Duplicates: versioned files with originals still in live dir (no no)
ls wgEncodeUtaChIPseqRawDataRep1Helas3Cmyc.fastq.gz
ls wgEncodeUtaChIPseqRawDataRep2Helas3Cmyc.fastq.gz
ls wgEncodeUtaChIPseqAlignmentsRep2Helas3Cmyc.tagAlign.gz
ls wgEncodeUtaChIPseqAlignmentsRep1Helas3Cmyc.tagAlign.gz
ls release1/wgEncodeUtaChIPseqRawDataRep1Helas3Cmyc.fastq.gz
ls release1/wgEncodeUtaChIPseqRawDataRep2Helas3Cmyc.fastq.gz
ls release1/wgEncodeUtaChIPseqAlignmentsRep2Helas3Cmyc.tagAlign.gz
ls release1/wgEncodeUtaChIPseqAlignmentsRep1Helas3Cmyc.tagAlign.gz
rm wgEncodeUtaChIPseqRawDataRep1Helas3Cmyc.fastq.gz
rm wgEncodeUtaChIPseqRawDataRep2Helas3Cmyc.fastq.gz
rm wgEncodeUtaChIPseqAlignmentsRep2Helas3Cmyc.tagAlign.gz
rm wgEncodeUtaChIPseqAlignmentsRep1Helas3Cmyc.tagAlign.gz
encodeDownloadsPage.pl index.html 

# edit preamble.html to add release note.
encodeDownloadsPage.pl index.html

cd {downloadsDir}
mkdir release2
cd release2 
cp ../index.html .
cp ../preamble.html .
cp ../fileDb.ra .
ls -1 ../*.gz | wl  318
ln ../*.gz .   
ls -1 *.gz | wl     318

drop table wgEncodeUncFAIREseqPeaksHelas3V2;
rename table wgEncodeUncFAIREseqPeaksRep1Helas3V2 to wgEncodeUncFAIREseqPeaksHelas3V2;
rename table wgEncodeUncFAIREseqPeaksRep1Nhek to wgEncodeUncFAIREseqPeaksNhek;
drop table wgEncodeUncFAIREseqPeaksK562V2;
rename table wgEncodeUncFAIREseqPeaksRep1K562V2 to wgEncodeUncFAIREseqPeaksK562V2;
ll wgEncodeUncFAIREseqPeaksRep1K562V2.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksRep1Helas3V2.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksRep1Nhek.narrowPeak.gz

rm wgEncodeUncFAIREseqPeaksRep1K562V2.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksRep1Helas3V2.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksRep1Nhek.narrowPeak.gz

cd ..
mv wgEncodeUncFAIREseqPeaksRep1K562V2.narrowPeak.gz wgEncodeUncFAIREseqPeaksK562V2.narrowPeak.gz
mv wgEncodeUncFAIREseqPeaksRep1Helas3V2.narrowPeak.gz wgEncodeUncFAIREseqPeaksHelas3V2.narrowPeak.gz
mv wgEncodeUncFAIREseqPeaksRep1Nhek.narrowPeak.gz wgEncodeUncFAIREseqPeaksNhek.narrowPeak.gz
cd release2/
ln ../wgEncodeUncFAIREseqPeaksK562V2.narrowPeak.gz .
ln ../wgEncodeUncFAIREseqPeaksHelas3V2.narrowPeak.gz .
ln ../wgEncodeUncFAIREseqPeaksNhek.narrowPeak.gz .
ll wgEncodeUncFAIREseqPeaksK562V2.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksHelas3V2.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksNhek.narrowPeak.gz

Problem names:
| wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12891 | 
| wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12892 | 
| wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19238 | 
| wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19239 | 
| wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19240 | 
| wgEncodeDukeDNaseSeqSignalRep1Gm12891            | 
| wgEncodeDukeDNaseSeqSignalRep1Gm12892            | 
| wgEncodeDukeDNaseSeqSignalRep1Gm19238            | 
| wgEncodeDukeDNaseSeqSignalRep1Gm19239            | 
| wgEncodeDukeDNaseSeqSignalRep1Gm19240            | 
| wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12891Ctcf  | 
| wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12892Ctcf  | 
| wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19238Ctcf  | 
| wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19239Ctcf  | 
| wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19240Ctcf  | 
| wgEncodeUtaChIPseqBaseOverlapSignalRep1Helas3CmycV2 | 
| wgEncodeUtaChIPseqSignalRep1Gm12891Ctcf             | 
| wgEncodeUtaChIPseqSignalRep1Gm12892Ctcf             | 
| wgEncodeUtaChIPseqSignalRep1Gm19238Ctcf             | 
| wgEncodeUtaChIPseqSignalRep1Gm19239Ctcf             | 
| wgEncodeUtaChIPseqSignalRep1Gm19240Ctcf             | 
| wgEncodeUtaChIPseqSignalRep1Helas3CmycV2            | 
| wgEncodeUncFAIREseqBaseOverlapSignalRep1Helas3V2 | 
| wgEncodeUncFAIREseqBaseOverlapSignalRep1K562V2   | 
| wgEncodeUncFAIREseqBaseOverlapSignalRep1Nhek     | 
| wgEncodeUncFAIREseqSignalRep1Helas3V2            | 
| wgEncodeUncFAIREseqSignalRep1K562V2              | 
| wgEncodeUncFAIREseqSignalRep1Nhek                | 

| wgEncodeDukeDNaseSeqPeaksRep1Gm12891             | 
| wgEncodeDukeDNaseSeqPeaksRep1Gm12892             | 
| wgEncodeDukeDNaseSeqPeaksRep1Gm19238             | 
| wgEncodeDukeDNaseSeqPeaksRep1Gm19239             | 
| wgEncodeDukeDNaseSeqPeaksRep1Gm19240             | 
| wgEncodeUtaChIPseqPeaksRep1Gm12891Ctcf              | 
| wgEncodeUtaChIPseqPeaksRep1Gm12892Ctcf              | 
| wgEncodeUtaChIPseqPeaksRep1Gm19238Ctcf              | 
| wgEncodeUtaChIPseqPeaksRep1Gm19239Ctcf              | 
| wgEncodeUtaChIPseqPeaksRep1Gm19240Ctcf              | 
| wgEncodeUtaChIPseqPeaksRep1Helas3CmycV2             | 

rename table wgEncodeDukeDNaseSeqPeaksRep1Gm12891    to wgEncodeDukeDNaseSeqPeaksGm12891;
rename table wgEncodeDukeDNaseSeqPeaksRep1Gm12892    to wgEncodeDukeDNaseSeqPeaksGm12892;
rename table wgEncodeDukeDNaseSeqPeaksRep1Gm19238    to wgEncodeDukeDNaseSeqPeaksGm19238;
rename table wgEncodeDukeDNaseSeqPeaksRep1Gm19239    to wgEncodeDukeDNaseSeqPeaksGm19239;
rename table wgEncodeDukeDNaseSeqPeaksRep1Gm19240    to wgEncodeDukeDNaseSeqPeaksGm19240;
rename table wgEncodeUtaChIPseqPeaksRep1Gm12891Ctcf  to wgEncodeUtaChIPseqPeaksGm12891Ctcf;
rename table wgEncodeUtaChIPseqPeaksRep1Gm12892Ctcf  to wgEncodeUtaChIPseqPeaksGm12892Ctcf;
rename table wgEncodeUtaChIPseqPeaksRep1Gm19238Ctcf  to wgEncodeUtaChIPseqPeaksGm19238Ctcf;
rename table wgEncodeUtaChIPseqPeaksRep1Gm19239Ctcf  to wgEncodeUtaChIPseqPeaksGm19239Ctcf;
rename table wgEncodeUtaChIPseqPeaksRep1Gm19240Ctcf  to wgEncodeUtaChIPseqPeaksGm19240Ctcf;
rename table wgEncodeUtaChIPseqPeaksRep1Helas3CmycV2 to wgEncodeUtaChIPseqPeaksHelas3CmycV2;

mv wgEncodeDukeDNaseSeqPeaksRep1Gm12891.narrowPeak.gz    wgEncodeDukeDNaseSeqPeaksGm12891.narrowPeak.gz
mv wgEncodeDukeDNaseSeqPeaksRep1Gm12892.narrowPeak.gz    wgEncodeDukeDNaseSeqPeaksGm12892.narrowPeak.gz
mv wgEncodeDukeDNaseSeqPeaksRep1Gm19238.narrowPeak.gz    wgEncodeDukeDNaseSeqPeaksGm19238.narrowPeak.gz
mv wgEncodeDukeDNaseSeqPeaksRep1Gm19239.narrowPeak.gz    wgEncodeDukeDNaseSeqPeaksGm19239.narrowPeak.gz
mv wgEncodeDukeDNaseSeqPeaksRep1Gm19240.narrowPeak.gz    wgEncodeDukeDNaseSeqPeaksGm19240.narrowPeak.gz
mv wgEncodeUtaChIPseqPeaksRep1Gm12891Ctcf.narrowPeak.gz  wgEncodeUtaChIPseqPeaksGm12891Ctcf.narrowPeak.gz
mv wgEncodeUtaChIPseqPeaksRep1Gm12892Ctcf.narrowPeak.gz  wgEncodeUtaChIPseqPeaksGm12892Ctcf.narrowPeak.gz
mv wgEncodeUtaChIPseqPeaksRep1Gm19238Ctcf.narrowPeak.gz  wgEncodeUtaChIPseqPeaksGm19238Ctcf.narrowPeak.gz
mv wgEncodeUtaChIPseqPeaksRep1Gm19239Ctcf.narrowPeak.gz  wgEncodeUtaChIPseqPeaksGm19239Ctcf.narrowPeak.gz
mv wgEncodeUtaChIPseqPeaksRep1Gm19240Ctcf.narrowPeak.gz  wgEncodeUtaChIPseqPeaksGm19240Ctcf.narrowPeak.gz
mv wgEncodeUtaChIPseqPeaksRep1Helas3CmycV2.narrowPeak.gz wgEncodeUtaChIPseqPeaksHelas3CmycV2.narrowPeak.gz

drop table wgEncodeUncFAIREseqBaseOverlapSignalHelas3V2;
rm /gbdb/hg18/wib/wgEncodeUncFAIREseqBaseOverlapSignalHelas3V2.wib
drop table wgEncodeUncFAIREseqBaseOverlapSignalK562V2;
rm /gbdb/hg18/wib/wgEncodeUncFAIREseqBaseOverlapSignalK562V2.wib
drop table wgEncodeUncFAIREseqSignalHelas3V2;
rm /gbdb/hg18/wib/wgEncodeUncFAIREseqSignalHelas3V2.wib
drop table wgEncodeUncFAIREseqSignalK562V2;
rm /gbdb/hg18/wib/wgEncodeUncFAIREseqSignalK562V2.wib

rename table wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12891    to wgEncodeDukeDNaseSeqBaseOverlapSignalGm12891   ;
rename table wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12892    to wgEncodeDukeDNaseSeqBaseOverlapSignalGm12892   ;
rename table wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19238    to wgEncodeDukeDNaseSeqBaseOverlapSignalGm19238   ;
rename table wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19239    to wgEncodeDukeDNaseSeqBaseOverlapSignalGm19239   ;
rename table wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19240    to wgEncodeDukeDNaseSeqBaseOverlapSignalGm19240   ;
rename table wgEncodeDukeDNaseSeqSignalRep1Gm12891               to wgEncodeDukeDNaseSeqSignalGm12891              ;
rename table wgEncodeDukeDNaseSeqSignalRep1Gm12892               to wgEncodeDukeDNaseSeqSignalGm12892              ;
rename table wgEncodeDukeDNaseSeqSignalRep1Gm19238               to wgEncodeDukeDNaseSeqSignalGm19238              ;
rename table wgEncodeDukeDNaseSeqSignalRep1Gm19239               to wgEncodeDukeDNaseSeqSignalGm19239              ;
rename table wgEncodeDukeDNaseSeqSignalRep1Gm19240               to wgEncodeDukeDNaseSeqSignalGm19240              ;
rename table wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12891Ctcf  to wgEncodeUtaChIPseqBaseOverlapSignalGm12891Ctcf ;
rename table wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12892Ctcf  to wgEncodeUtaChIPseqBaseOverlapSignalGm12892Ctcf ;
rename table wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19238Ctcf  to wgEncodeUtaChIPseqBaseOverlapSignalGm19238Ctcf ;
rename table wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19239Ctcf  to wgEncodeUtaChIPseqBaseOverlapSignalGm19239Ctcf ;
rename table wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19240Ctcf  to wgEncodeUtaChIPseqBaseOverlapSignalGm19240Ctcf ;
rename table wgEncodeUtaChIPseqBaseOverlapSignalRep1Helas3CmycV2 to wgEncodeUtaChIPseqBaseOverlapSignalHelas3CmycV2;
rename table wgEncodeUtaChIPseqSignalRep1Gm12891Ctcf             to wgEncodeUtaChIPseqSignalGm12891Ctcf            ;
rename table wgEncodeUtaChIPseqSignalRep1Gm12892Ctcf             to wgEncodeUtaChIPseqSignalGm12892Ctcf            ;
rename table wgEncodeUtaChIPseqSignalRep1Gm19238Ctcf             to wgEncodeUtaChIPseqSignalGm19238Ctcf            ;
rename table wgEncodeUtaChIPseqSignalRep1Gm19239Ctcf             to wgEncodeUtaChIPseqSignalGm19239Ctcf            ;
rename table wgEncodeUtaChIPseqSignalRep1Gm19240Ctcf             to wgEncodeUtaChIPseqSignalGm19240Ctcf            ;
rename table wgEncodeUtaChIPseqSignalRep1Helas3CmycV2            to wgEncodeUtaChIPseqSignalHelas3CmycV2           ;
rename table wgEncodeUncFAIREseqBaseOverlapSignalRep1Helas3V2    to wgEncodeUncFAIREseqBaseOverlapSignalHelas3V2   ;
rename table wgEncodeUncFAIREseqBaseOverlapSignalRep1K562V2      to wgEncodeUncFAIREseqBaseOverlapSignalK562V2     ;
rename table wgEncodeUncFAIREseqBaseOverlapSignalRep1Nhek        to wgEncodeUncFAIREseqBaseOverlapSignalNhek       ;
rename table wgEncodeUncFAIREseqSignalRep1Helas3V2               to wgEncodeUncFAIREseqSignalHelas3V2              ;
rename table wgEncodeUncFAIREseqSignalRep1K562V2                 to wgEncodeUncFAIREseqSignalK562V2                ;
rename table wgEncodeUncFAIREseqSignalRep1Nhek                   to wgEncodeUncFAIREseqSignalNhek                  ;

cd {dowloadsDir}
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12891.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm12891.wig.gz
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12892.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm12892.wig.gz
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19238.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm19238.wig.gz
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19239.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm19239.wig.gz
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19240.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm19240.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm12891.wig.gz               wgEncodeDukeDNaseSeqSignalGm12891.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm12892.wig.gz               wgEncodeDukeDNaseSeqSignalGm12892.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm19238.wig.gz               wgEncodeDukeDNaseSeqSignalGm19238.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm19239.wig.gz               wgEncodeDukeDNaseSeqSignalGm19239.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm19240.wig.gz               wgEncodeDukeDNaseSeqSignalGm19240.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12891Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm12891Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12892Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm12892Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19238Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm19238Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19239Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm19239Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19240Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm19240Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Helas3CmycV2.wig.gz wgEncodeUtaChIPseqBaseOverlapSignalHelas3CmycV2.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm12891Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm12891Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm12892Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm12892Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm19238Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm19238Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm19239Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm19239Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm19240Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm19240Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Helas3CmycV2.wig.gz            wgEncodeUtaChIPseqSignalHelas3CmycV2.wig.gz
mv wgEncodeUncFAIREseqBaseOverlapSignalRep1Helas3V2.wig.gz    wgEncodeUncFAIREseqBaseOverlapSignalHelas3V2.wig.gz
mv wgEncodeUncFAIREseqBaseOverlapSignalRep1K562V2.wig.gz      wgEncodeUncFAIREseqBaseOverlapSignalK562V2.wig.gz
mv wgEncodeUncFAIREseqBaseOverlapSignalRep1Nhek.wig.gz        wgEncodeUncFAIREseqBaseOverlapSignalNhek.wig.gz
mv wgEncodeUncFAIREseqSignalRep1Helas3V2.wig.gz               wgEncodeUncFAIREseqSignalHelas3V2.wig.gz
mv wgEncodeUncFAIREseqSignalRep1K562V2.wig.gz                 wgEncodeUncFAIREseqSignalK562V2.wig.gz
mv wgEncodeUncFAIREseqSignalRep1Nhek.wig.gz                   wgEncodeUncFAIREseqSignalNhek.wig.gz

cd release2/
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12891.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm12891.wig.gz
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm12892.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm12892.wig.gz
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19238.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm19238.wig.gz
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19239.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm19239.wig.gz
mv wgEncodeDukeDNaseSeqBaseOverlapSignalRep1Gm19240.wig.gz    wgEncodeDukeDNaseSeqBaseOverlapSignalGm19240.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm12891.wig.gz               wgEncodeDukeDNaseSeqSignalGm12891.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm12892.wig.gz               wgEncodeDukeDNaseSeqSignalGm12892.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm19238.wig.gz               wgEncodeDukeDNaseSeqSignalGm19238.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm19239.wig.gz               wgEncodeDukeDNaseSeqSignalGm19239.wig.gz
mv wgEncodeDukeDNaseSeqSignalRep1Gm19240.wig.gz               wgEncodeDukeDNaseSeqSignalGm19240.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12891Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm12891Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm12892Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm12892Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19238Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm19238Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19239Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm19239Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Gm19240Ctcf.wig.gz  wgEncodeUtaChIPseqBaseOverlapSignalGm19240Ctcf.wig.gz
mv wgEncodeUtaChIPseqBaseOverlapSignalRep1Helas3CmycV2.wig.gz wgEncodeUtaChIPseqBaseOverlapSignalHelas3CmycV2.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm12891Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm12891Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm12892Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm12892Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm19238Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm19238Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm19239Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm19239Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Gm19240Ctcf.wig.gz             wgEncodeUtaChIPseqSignalGm19240Ctcf.wig.gz
mv wgEncodeUtaChIPseqSignalRep1Helas3CmycV2.wig.gz            wgEncodeUtaChIPseqSignalHelas3CmycV2.wig.gz
mv wgEncodeUncFAIREseqBaseOverlapSignalRep1Helas3V2.wig.gz    wgEncodeUncFAIREseqBaseOverlapSignalHelas3V2.wig.gz
mv wgEncodeUncFAIREseqBaseOverlapSignalRep1K562V2.wig.gz      wgEncodeUncFAIREseqBaseOverlapSignalK562V2.wig.gz
mv wgEncodeUncFAIREseqBaseOverlapSignalRep1Nhek.wig.gz        wgEncodeUncFAIREseqBaseOverlapSignalNhek.wig.gz
mv wgEncodeUncFAIREseqSignalRep1Helas3V2.wig.gz               wgEncodeUncFAIREseqSignalHelas3V2.wig.gz
mv wgEncodeUncFAIREseqSignalRep1K562V2.wig.gz                 wgEncodeUncFAIREseqSignalK562V2.wig.gz
mv wgEncodeUncFAIREseqSignalRep1Nhek.wig.gz                   wgEncodeUncFAIREseqSignalNhek.wig.gz

# edit trackDb.wgEncode.ra with table name 
make alpha DBS=hg18

# update downloads Dir
cd {downloadsDir}
encodeDownloadsPage.pl index.html
cp index.html release2/

### FINALLY put release2 into the pushQ

Versioned:
# submission 461 (versioning by 277)
# submission 471  (versioning by 287)
# submission 468 (versioning 278)
# submission 495 (versioning 280)
# submission 639 (versioning 336, replacing 494) 494 marked superseded
# submission 493 (versioning 281)
# submission 642 (versioning 282)
# submission 556 (versioning 277)
# submission 557 (versioning 286)
# submission 555 (versioning 283)
# submission 593 (versioning 284)
# submission 480 (versioning 235,277,116)
# submission 640 (versioning 287, replacing 483) 483 marked superseded
# submission 481 (versioning 278,244)
# submission 482 (versioning 278,245)
### The versioned ones could be superseded when release2 goes public

2009-11-03 Resubmision of base overlaps
=======================================
# fix minor validation problems and add "allowReload" to DAFs for 762,763,764,765,766,767
# Update trackDb with new subIds and dateResubmitted
# Not submitted??
wgEncodeUtaChIPseqBaseOverlapSignalGm12878Cmyc
wgEncodeUtaChIPseqBaseOverlapSignalH1hescPol2
wgEncodeUtaChIPseqBaseOverlapSignalHepg2Pol2
wgEncodeUtaChIPseqBaseOverlapSignalHuvecCmyc
wgEncodeUtaChIPseqBaseOverlapSignalHuvecPol2
wgEncodeUtaChIPseqBaseOverlapSignalK562Pol2
# confirmed that these are missing in the bowser on chrX

cvs ci trackDb.wgEncode.ra
make alpha DBS=hg18

# Now update downloadsDir
cd {downloadsDir}
ll *Base*.gz 
# All show 2 links: one in root, one in release2/
ll *Base*.gz | wl                              41
ll release2/*Base*.gz | wl                     41
ll *Base*.gz | grep "2 qateam" | wl            41
ll release2/*Base*.gz | grep "2 qateam" | wl   41

mv ../wgEncodeDukeDNaseSeq/*Base*.gz .
ll *Base*.gz | grep "2 qateam" | wl            29
ll *Base*.gz | grep "1 qateam" | wl            12

mv ../wgEncodeUncFAIREseq/*Base*.gz .
ll *Base*.gz | grep "2 qateam" | wl            21
ll *Base*.gz | grep "1 qateam" | wl            20

mv ../wgEncodeUt-aChIPseq/*Base*.gz .
ll *Base*.gz | grep "2 qateam" | wl             6
ll *Base*.gz | grep "1 qateam" | wl            35

# Now fix release2/
cd release2/
ll *Base*.gz | grep "2 qateam" | wl             6
ll *Base*.gz | grep "1 qateam" | wl            35
ln ../*Base*.gz . 
ll *Base*.gz | grep "2 qateam" | wl             6
ll *Base*.gz | grep "1 qateam" | wl            35
# doesn't work, since file is in the way.
rm *Base*.gz
ln ../*Base*.gz . 
ll *Base*.gz | grep "2 qateam" | wl            41
ll *Base*.gz | grep "1 qateam" | wl             0
cd ..
ll *Base*.gz | grep "2 qateam" | wl            41
ll *Base*.gz | grep "1 qateam" | wl             0
# success

# No need to update fileDb, as BO are all tables
encodeDownloadsPage.pl index.html

/cluster/data/encode/pipeline/bin/encodeStatus.pl 762 displayed
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2009-11-06 Major screwup. REPAIR
================================
# last 7 submissions were for BO chrX and chrY, but did not include chrs 1-22!
# Get files from previous submissions:
cd {pip}/770
cd HUVEC/Pol2
ls
ls ../../../552/ucsc/*BaseOverlap*.wig
# makes a set
mv ../../../552/ucsc/*BaseOverlap*.wig .
cd ../c-Myc
ls
ls ../../../635/uc/*BaseOverlap*.wig
mv ../../../635/ucsc/*BaseOverlap*.wig .
cd ../../GM12878/c-Myc
ls
ls ../../../472/ucsc/*BaseOverlap*.wig
mv ../../../472/ucsc/*BaseOverlap*.wig .
cd ../K562/Pol2
ls
ls ../../../588/ucsc/*BaseOverlap*.wig
mv ../../../588/ucsc/*BaseOverlap*.wig .
cd ../H1-hESC/Pol2
ls
ls ../../../641/ucsc/*BaseOverlap*.wig
mv ../../../641/ucsc/*BaseOverlap*.wig .
# unload and resubmit
cd {pip}/766
cd GM12891/CTCF
ls
ls ../../../644/ucsc/*BaseOverlap*.wig
mv ../../../644/ucsc/*BaseOverlap*.wig .
cd ../../GM12892/CTCF
ls
ls ../../../638/ucsc/*BaseOverlap*.wig
mv ../../../638/ucsc/*BaseOverlap*.wig .  ### WARNING only chr1 and chrX found!!!
cd ../../GM19238/CTCF
ls
ls ../../../646/ucsc/*BaseOverlap*.wig
mv ../../../646/ucsc/*BaseOverlap*.wig .  
cd ../../GM19239/CTCF
ls
ls ../../../648/ucsc/*BaseOverlap*.wig
mv ../../../648/ucsc/*BaseOverlap*.wig .  
cd ../../GM19240/CTCF
ls
ls ../../../650/ucsc/*BaseOverlap*.wig
mv ../../../650/ucsc/*BaseOverlap*.wig .  
cd ../../H1-hESC/CTCF
ls
ls ../../../636/ucsc/*BaseOverlap*.wig
mv ../../../636/ucsc/*BaseOverlap*.wig .  
cd ../../HUVEC/CTCF
ls
ls ../../../548/ucsc/*BaseOverlap*.wig
mv ../../../548/ucsc/*BaseOverlap*.wig .  
cd ../../NHEK/CTCF
ls
ls ../../../624/ucsc/*BaseOverlap*.wig
mv ../../../624/ucsc/*BaseOverlap*.wig .  
# unload and resubmit
cd {pip}/767
cd GM12878/CTCF
ls
ls ../../../468/ucsc/*BaseOverlap*.wig
mv ../../../468/ucsc/*BaseOverlap*.wig .  
cd ../../HeLa-S3/CTCF
ls
ls ../../../493/ucsc/*BaseOverlap*.wig
mv ../../../493/ucsc/*BaseOverlap*.wig .  
cd ../c-Myc
ls
ls ../../../642/ucsc/*BaseOverlap*.wig
mv ../../../642/ucsc/*BaseOverlap*.wig .  
cd ../../HepG2/CTCF
ls
ls ../../../555/ucsc/*BaseOverlap*.wig
mv ../../../555/ucsc/*BaseOverlap*.wig .  
cd ../c-Myc
ls
ls ../../../593/ucsc/*BaseOverlap*.wig
mv ../../../593/ucsc/*BaseOverlap*.wig .  
cd ../../K562/CTCF
ls
ls ../../../481/ucsc/*BaseOverlap*.wig
mv ../../../481/ucsc/*BaseOverlap*.wig .  
cd ../c-Myc
ls
ls ../../../482/ucsc/*BaseOverlap*.wig
mv ../../../482/ucsc/*BaseOverlap*.wig .  
# unload and resubmit
cd {pip}/764
cd H1-hESC
ls
ls ../../629/ucsc/*BaseOverlap*.wig
mv ../../629/ucsc/*BaseOverlap*.wig .  
cd ../HUVEC
ls
ls ../../546/ucsc/*BaseOverlap*.wig
mv ../../546/ucsc/*BaseOverlap*.wig .  
cd ../NHEK
ls
ls ../../630/ucsc/*BaseOverlap*.wig
mv ../../630/ucsc/*BaseOverlap*.wig .  
cd ../PanIslets
ls
ls ../../686/ucsc/*BaseOverlap*.wig
mv ../../686/ucsc/*BaseOverlap*.wig .  
# unload and resubmit
cd {pip}/765
cd GM12878
ls
ls ../../471/ucsc/*BaseOverlap*.wig
mv ../../471/ucsc/*BaseOverlap*.wig .  
cd ../HeLa-S3
ls
ls ../../639/ucsc/*BaseOverlap*.wig
mv ../../639/ucsc/*BaseOverlap*.wig .  
cd ../HepG2
ls
ls ../../557/ucsc/*BaseOverlap*.wig
mv ../../557/ucsc/*BaseOverlap*.wig .  
cd ../K562
ls
ls ../../640/ucsc/*BaseOverlap*.wig
mv ../../640/ucsc/*BaseOverlap*.wig .  
# unload and resubmit
cd {pip}/762
cd GM12891
ls
ls ../../643/ucsc/*BaseOverlap*.wig
mv ../../643/ucsc/*BaseOverlap*.wig .  
cd ../GM12892
ls
ls ../../645/ucsc/*BaseOverlap*.wig
mv ../../645/ucsc/*BaseOverlap*.wig .  
cd ../GM19238
ls
ls ../../647/ucsc/*BaseOverlap*.wig
mv ../../647/ucsc/*BaseOverlap*.wig .  
cd ../GM19239
ls
ls ../../649/ucsc/*BaseOverlap*.wig
mv ../../649/ucsc/*BaseOverlap*.wig .  
cd ../GM19240
ls
ls ../../651/ucsc/*BaseOverlap*.wig
mv ../../651/ucsc/*BaseOverlap*.wig .  
cd ../H1-hESC
ls
ls ../../628/ucsc/*BaseOverlap*.wig
mv ../../628/ucsc/*BaseOverlap*.wig .  
cd ../HUVEC
ls
ls ../../545/ucsc/*BaseOverlap*.wig
mv ../../545/ucsc/*BaseOverlap*.wig .  
cd ../NHEK
ls
ls ../../594/ucsc/*BaseOverlap*.wig
mv ../../594/ucsc/*BaseOverlap*.wig .  
# unload and resubmit
cd {pip}/763
cd GM12878
ls
ls ../../461/ucsc/*BaseOverlap*.wig
mv ../../461/ucsc/*BaseOverlap*.wig .  
cd ../HeLa-S3
ls
ls ../../495/ucsc/*BaseOverlap*.wig
mv ../../495/ucsc/*BaseOverlap*.wig .  ### WARNING  Does not have chrX !  Original submission of chrX was labelled H1_ES
cd ../HepG2
ls
ls ../../556/ucsc/*BaseOverlap*.wig
mv ../../556/ucsc/*BaseOverlap*.wig .  
cd ../K562
ls
ls ../../480/ucsc/*BaseOverlap*.wig
mv ../../480/ucsc/*BaseOverlap*.wig .  
# unload and resubmit

# Update downloads:
cd {downloadsDir}
mv ../wgEncodeUncFAIREseq/*.gz .
cd release2/
ls ../wgEncodeUncFAIREseqBaseOverlapSignal*.gz 
rm wgEncodeUncFAIREseqBaseOverlapSignal*.gz 
ln ../wgEncodeUncFAIREseqBaseOverlapSignal*.gz .


cv {downloadsDir}
mv /hive/groups/encode/dcc/pipeline/encpipeline_prod/764/wgEncodeUncFAIREseqBaseOverlapSignal*.gz .
mv /hive/groups/encode/dcc/pipeline/encpipeline_prod/765/wgEncodeUncFAIREseqBaseOverlapSignal*.gz .
cd release2/
ll wgEncodeUncFAIREseqBaseOverlapSignal*.gz # 8 singlr link
ll ../wgEncodeUncFAIREseqBaseOverlapSignal*.gz # 8
rm wgEncodeUncFAIREseqBaseOverlapSignal*.gz
ln ../wgEncodeUncFAIREseqBaseOverlapSignal*.gz .
ll wgEncodeUncFAIREseqBaseOverlapSignal*.gz # 8 double linked

cd ..
ll ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignal*.gz | wl # 20
ll wgEncodeUtaChIPseqBaseOverlapSignal*.gz | wl # doubly linked 21  HepG2/Pol2
mv ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignal*.gz .
cd release2/
ll wgEncodeUtaChIPseqBaseOverlapSignal*.gz | wl # single linked 20, doubly HepG2/Pol2
ll ../wgEncodeUtaChIPseqBaseOverlapSignal*.gz | wl # single linked 20, doubly HepG2/Pol2
rm wgEncodeUtaChIPseqBaseOverlapSignal*.gz
ln ../wgEncodeUtaChIPseqBaseOverlapSignal*.gz .
ll ../wgEncodeUtaChIPseqBaseOverlapSignal*.gz | wl # double linked 21 HepG2/Pol2

cd ..
ll ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz | wl # 12
ll wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz | wl # 12 doubly linked
mv ../wgEncodeDukeDNaseSeq/wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz .
ll wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz | wl # 12 singly linked
cd release2/
ll wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz | wl # 12 singly linked
ll ../wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz | wl # 12 singly linked
rm wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz 
ln ../wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz .
ll ../wgEncodeDukeDNaseSeqBaseOverlapSignal*.gz | wl # 12 doubly linked

## The submission of the missing HepG2/Pol2 773
cd 773
cd HepG2
ls
ls ../589/ucsc/HepG2_UtaChIPseq_PolII_BaseOverlap_chr*.wig
mv ../589/ucsc/HepG2_UtaChIPseq_PolII_BaseOverlap_chr*.wig .
# allowReloads and resubmit

# Edit trackDb.wgEncode.ra with 770,771,772,773
# confirm all BO wig values are correct (several needed fixing)
# confirm all BO and FD viewLimits are correct (all were correct)
make alpha DBS=hg18

# fix up downloads dir
cd {downloadDir}
ll wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalHepg2Pol2.wig.gz 
ll ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalHepg2Pol2.wig.gz 
mv ../wgEncodeUt-aChIPseq/wgEncodeUtaChIPseqBaseOverlapSignalHepg2Pol2.wig.gz .
cd release2/
rm wgEncodeUtaChIPseqBaseOverlapSignalHepg2Pol2.wig.gz 
ln ../wgEncodeUtaChIPseqBaseOverlapSignalHepg2Pol2.wig.gz .
cd ..
encodeDownloadsPage.pl index.html
cp index.html release2/
# verify subId=773 on index.html

/cluster/data/encode/pipeline/bin/encodeStatus.pl 762 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 763 displayed
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 773 displayed

### At this point all issues for Open Chromatin release 2 should be closed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 461 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 468 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 471 approved
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 480 approved
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 765 approved
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 461 reviewing
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 471 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 472 reviewing
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 649 reviewing
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 651 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 686 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 762 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 763 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 764 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 765 reviewing
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 772 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 773 reviewing

2009-12-14 Released "Release 2"
===============================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 104 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 336 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 461 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 468 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 472 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 471 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 481 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 480 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 482 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 493 released
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 548 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 552 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 555 released
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 686 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 770 released
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/cluster/data/encode/pipeline/bin/encodeStatus.pl 772 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 773 released

2009-12-17 Beginning of Jan 2010 freeze!
========================================
# Incoming is private data which will have no sequence in tagAligns
# fails on validateFiles.  First error chopByWhile() instead of chopByTab()
~/bin/x86_64/validateFiles -type=tagAlign -chromDb=hg18 -genome=/cluster/data/hg18/hg18.2bit -quick=10 -privateData Raw_FB0167P_DukeDNaseSeq_rep1.taf

# 831 DNCT Duke DNaseHS Medullo 20091216
# 834 DNCT Duke DNaseHS ProgFib 20091217
# 835 DNCT Duke DNaseHS PanIslets 20091217
# 836 DNCT Duke DNaseHS HeLa-S3 IFNa4h 20091217
# 847 DNCT UNC FAIRE-Seq GM19239 20091218
# 848 DNCT Duke DNaseHS LHSR 20091218
# 849 DNCT Duke DNaseHS MCF-7 20091218
# 850 DNCT Duke DNaseHS GM18507 20091218
# 851 DNCT Duke DNaseHS LHSR androgen 20091218
# 852 DNCT UNC FAIRE-Seq GM18507 20091219
# 855 DNCT Duke DNaseHS Myoblast 20091219
# 856 DNCT Duke DNaseHS Myotube 20091219
# 857 DNCT Duke DNaseHS Fibrobla 20091220
# 858 DNCT UNC FAIRE-Seq HelaS3 IFNA 20091219
# 859 DNCT UNC FAIRE-Seq HelaS3 IFNG 20091219
# 866 DNCT UTA Input MCF-7 20091222
# 868 DNCT UTA PolII GM12878 20091222
# 871 DNCT UTA Input ProgFib 20091222
# 873 DNCT UNC FAIRE-Seq LHSR 20091222
# 874 DNCT UNC FAIRE-Seq LHSR androgen 20091222
# 877 DNCT Duke DNaseHS H9ES 20091223
# 881 DNCT Duke DNaseHS Chorion 20091227
# 882 DNCT UTA c-Myc H1_hESC 20091227
# 883 DNCT UTA c-Myc MCF-7 20091227
# 884 DNCT UTA CTCF MCF-7 20091227
# 885 DNCT UTA PolII HeLa-S3 20091228
# 886 DNCT UTA CTCF ProgFib 20100101
e /hive/groups/encode/dcc/pipeline/encpipeline_prod/831/out/trackDb.ra ...

encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/831/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/834/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/835/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/836/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/847/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/848/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/849/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/850/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/851/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/852/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/855/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/856/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/857/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/858/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/859/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/866/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/868/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/871/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/873/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/874/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/877/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/881/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/882/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/883/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/884/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/885/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb /hive/groups/encode/dcc/pipeline/encpipeline_prod/886/out/trackDb.ra trackDb.wgEncode.ra

cd {downloadsDir}
cp fileDb.ra fileDb.ra.2010-10-06
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/831/out/fileDb.ra | grep parentTable >  tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/834/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/835/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/836/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/847/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/848/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/849/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/850/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/851/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/852/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/855/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/856/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/857/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/858/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/859/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/866/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/868/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/871/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/873/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/874/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/877/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/881/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/882/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/883/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/884/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/885/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/886/out/fileDb.ra | grep parentTable >> tmp.txt
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html

### Melissa is doing the trackDb updates for the last set.  Terry takes the silver.

Advice for Melissa:
Download dir:
# go to download dir:
cd /usr/local/apache/htdocs/goldenPath/hg18/encodeDCC/wgEncodeChromatinMap
# Save the fileDb.ra file before altering it:
cp fileDb.ra fileDb.ra.2010-01-14
# Gather all the download only metadata lines from the submission dirs:
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/939/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata ...
# examine the metadata and edit as needed (I don't think you will have any that needs to be edited)
# add to the loacl fileDb.ra (APPEND is very important here)
cat tmp.txt >> fileDb.ra
# make the html page
encodeDonwlasPage.pl index.html
# examine the page in the browser.  Look for any files (likely at the bottom) which have no metadata
# if all is well mark all submission dirs as displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 939 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl ...
  
### 2010-01-20 Melissa reports that she has all the Open Chromatin submissions displayed!


## At the freeze:
select id,name,status, created_at from projects where user_id = 17 and created_at > date('2009-12-01');
+-----+-------------------------------------------+-----------+---------------------+
| id  | name                                      | status    | created_at          |
+-----+-------------------------------------------+-----------+---------------------+
| 939 | DNCT Duke DNaseHS AoSMC SFM 20100108      | displayed | 2010-01-08 18:31:51 | 
| 881 | DNCT Duke DNaseHS Chorion 20091227        | displayed | 2009-12-27 17:35:57 | 
| 857 | DNCT Duke DNaseHS Fibrobla 20091220       | displayed | 2009-12-20 05:57:18 | 
| 960 | DNCT Duke DNaseHS FibroP 20100109         | displayed | 2010-01-09 16:56:29 | 
| 850 | DNCT Duke DNaseHS GM18507 20091218        | displayed | 2009-12-18 19:28:40 | 
| 877 | DNCT Duke DNaseHS H9ES 20091223           | displayed | 2009-12-23 19:15:10 | 
| 836 | DNCT Duke DNaseHS HeLa-S3 IFNa4h 20091217 | displayed | 2009-12-18 05:37:27 | 
| 848 | DNCT Duke DNaseHS LHSR 20091218           | displayed | 2009-12-18 13:42:02 | 
| 851 | DNCT Duke DNaseHS LHSR androgen 20091218  | displayed | 2009-12-18 19:55:55 | 
| 849 | DNCT Duke DNaseHS MCF-7 20091218          | displayed | 2009-12-18 14:13:22 | 
| 831 | DNCT Duke DNaseHS Medullo 20091216        | displayed | 2009-12-16 14:44:25 | 
| 953 | DNCT Duke DNaseHS Melano 20100108         | displayed | 2010-01-09 04:08:55 | 
| 855 | DNCT Duke DNaseHS Myoblast 20091219       | displayed | 2009-12-19 20:22:04 | 
| 940 | DNCT Duke DNaseHS Myometr 20100108        | displayed | 2010-01-08 18:32:45 | 
| 856 | DNCT Duke DNaseHS Myotube 20091219        | displayed | 2009-12-19 20:56:33 | 
| 835 | DNCT Duke DNaseHS PanIslets 20091217      | displayed | 2009-12-17 11:19:05 | 
| 834 | DNCT Duke DNaseHS ProgFib 20091217        | displayed | 2009-12-17 06:02:07 | 
| 852 | DNCT UNC FAIRE-Seq GM18507 20091219       | displayed | 2009-12-19 15:55:20 | 
| 847 | DNCT UNC FAIRE-Seq GM19239 20091218       | displayed | 2009-12-18 13:41:10 | 
| 858 | DNCT UNC FAIRE-Seq HelaS3 IFNA 20091219   | displayed | 2009-12-20 06:35:34 | 
| 859 | DNCT UNC FAIRE-Seq HelaS3 IFNG 20091219   | displayed | 2009-12-20 06:40:12 | 
| 873 | DNCT UNC FAIRE-Seq LHSR 20091222          | displayed | 2009-12-22 18:03:01 | 
| 874 | DNCT UNC FAIRE-Seq LHSR androgen 20091222 | displayed | 2009-12-23 04:17:48 | 
| 955 | DNCT UNC FAIRE-Seq NHBE 20100108          | displayed | 2010-01-09 04:10:55 | 
| 882 | DNCT UTA c-Myc H1_hESC 20091227           | displayed | 2009-12-27 18:06:21 | 
| 883 | DNCT UTA c-Myc MCF-7 20091227             | displayed | 2009-12-28 07:16:35 | 
| 884 | DNCT UTA CTCF MCF-7 20091227              | displayed | 2009-12-28 07:17:18 | 
| 886 | DNCT UTA CTCF ProgFib 20100101            | displayed | 2010-01-02 07:57:08 | 
| 866 | DNCT UTA Input MCF-7 20091222             | displayed | 2009-12-22 12:23:16 | 
| 871 | DNCT UTA Input ProgFib 20091222           | displayed | 2009-12-22 17:53:14 | 
| 868 | DNCT UTA PolII GM12878 20091222           | displayed | 2009-12-22 16:28:37 | 
| 885 | DNCT UTA PolII HeLa-S3 20091228           | displayed | 2009-12-28 07:17:58 | 
| 969 | DNCT UTA PolII ProgFib 20100109           | displayed | 2010-01-10 07:31:02 | 
| 829 | DNCT_DukeExonArrays_20091216              | displayed | 2009-12-16 13:33:25 | 
+-----+-------------------------------------------+-----------+---------------------+
34 rows

### Phone call on Monday:
# Issues:
1) Inconsistent short label: fixed
2) "zinba" peaks for FAIRE:  On hold!
3) Version Sep 2009 peaks: Needed by DAC!
4) Minor display issues: Terry will send list
5) Three cell protocols just submitted for approval!

# Need to submit/version some older peaks
Create sub dirs as me
1097 DNCT Duke DNaseHS V2 Peaks 20100128
1098 DNCT Duke DNaseHS V3 Peaks 20100128
1099 DNCT UNC FAIRE-Seq V2 Peaks 20100128
1100 DNCT UNC FAIRE-Seq V3 Peaks 20100128
1101 DNCT UTA ChIP V2 Peaks 20100128
1102 DNCT UTA ChIP V3 Peaks 20100128
mv ftp'd archives into 1098 1100, 1102
cd 1097
tar -xzf 001_NewPeaks_DAF_DDF &
cd ../1098
tar -xzf 001_Duke_Peaks_V3.tgz &
cd ../1100
tar -xzf 001_UNC_Peaks_V3.tgz &
cd ../1102
tar -xzf 001_UTA_Peaks_V3.tgz &
cd ../1097
mv DukeDNaseSeqPeaksOnlyV3.* ../1098
mv UncFAIREseqPeaksOnlyV2.D* ../1099
mv UncFAIREseqPeaksOnlyV3.D* ../1100
mv UtaChIPseqPeaksOnlyV2.D* ../1101 
mv UtaChIPseqPeaksOnlyV3.D* ../1102
mkdir DNaseHS
cd ../1098
mv DNaseHS/GM12891_DNaseHS.pk ../1097/DNaseHS/
mv DNaseHS/GM12892_DNaseHS.pk ../1097/DNaseHS/
mv DNaseHS/GM19238_DNaseHS.pk ../1097/DNaseHS/
mv DNaseHS/GM19239_DNaseHS.pk ../1097/DNaseHS/
mv DNaseHS/GM19240_DNaseHS.pk ../1097/DNaseHS/
cd ../1099
mkdir FAIRE
mv ../1100/FAIRE/HUVEC_FAIRE.pk FAIRE/
mv ../1100/FAIRE/NHEK_FAIRE.pk FAIRE/
mv ../1100/FAIRE/H1ES_FAIRE.pk FAIRE/
cd ../1101
mkdir ChIP
mv ../1102/ChIP/HUVEC_CTCF.pk .
mv ../1102/ChIP/H1ES_CTCF.pk .
mv ../1102/ChIP/GM12891_CTCF.pk .
mv ../1102/ChIP/GM12892_CTCF.pk .
mv ../1102/ChIP/GM19238_CTCF.pk .
mv ../1102/ChIP/GM19239_CTCF.pk .
mv ../1102/ChIP/GM19240_CTCF.pk .
mv ../1102/ChIP/GM12878_cMyc.pk .
mv ../1102/ChIP/HUVEC_cMyc.pk .
mv ../1102/ChIP/K562_PolII.pk .
mv ../1102/ChIP/HepG2_PolII.pk .
mv ../1102/ChIP/HUVEC_PolII.pk .
mv ../1102/ChIP/H1ES_PolII.pk .

# Submitted
# edit trackDb entries for tags, composite, etc.
e ../1097/out/trackDb.ra ../1098/out/trackDb.ra ../1099/out/trackDb.ra ../1100/out/trackDb.ra ../1101/out/trackDb.ra ../1102/out/trackDb.ra

encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1097/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1098/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1099/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1100/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1101/out/trackDb.ra trackDb.wgEncode.ra
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/1102/out/trackDb.ra trackDb.wgEncode.ra
# edit trackDb.wgEncode.ra to remove older versions!
### Can't get make DBS=hg18 to work: tdbQuery -check rejects 2 OpenChromatins!
tdbQuery -check 'select count(*) from hg18' -root=/cluster/home/tdreszer/kent/src/hg/makeDb/trackDb
wgEncodeDukeDNaseSeqPeaksGm12878V2 is a subTrack of wgEncodeChromatinMapViewPeaks, but wgEncodeChromatinMapViewPeaks doesn't exist
in track wgEncodeDukeDNaseSeqPeaksGm12878V2 stanza starting line 1894 of /cluster/home/tdreszer/kent/src/hg/makeDb/trackDb/human/hg18/trackDb.wgEncode.ra
wgEncodeUncFAIREseqPeaksGm12878V2 is a subTrack of wgEncodeChromatinMapViewPeaks, but wgEncodeChromatinMapViewPeaks doesn't exist
...
### Solved by putting the alpha composite BEFORE the beta composite.  However, tdbQuery still has a bug.
# however, the tdbQuery bug should be solved by the same changes required to fix the problem requiring 2 composites!

cvs ci
make alpha DBS=hg18

# remove older versions from downloadsDir
mv wgEncodeDukeDNaseSeqPeaksHuvec       versioned
mv wgEncodeDukeDNaseSeqPeaksNhek        versioned
mv wgEncodeDukeDNaseSeqPeaksH1hesc      versioned
mv wgEncodeDukeDNaseSeqPeaksGm12891     versioned
mv wgEncodeDukeDNaseSeqPeaksGm12892     versioned
mv wgEncodeDukeDNaseSeqPeaksGm19238     versioned
mv wgEncodeDukeDNaseSeqPeaksGm19239     versioned
mv wgEncodeDukeDNaseSeqPeaksGm19240     versioned
mv wgEncodeDukeDNaseSeqPeaksGm12878V2   versioned
mv wgEncodeDukeDNaseSeqPeaksK562V2      versioned
mv wgEncodeDukeDNaseSeqPeaksHepg2V2     versioned
mv wgEncodeDukeDNaseSeqPeaksHelas3V2    versioned
mv wgEncodeUncFAIREseqPeaksHuvec        versioned
mv wgEncodeUncFAIREseqPeaksNhek         versioned
mv wgEncodeUncFAIREseqPeaksH1hesc       versioned
mv wgEncodeUncFAIREseqPeaksGm12878V2    versioned
mv wgEncodeUncFAIREseqPeaksK562V2       versioned
mv wgEncodeUncFAIREseqPeaksHepg2V2      versioned
mv wgEncodeUncFAIREseqPeaksHelas3V2     versioned
mv wgEncodeUtaChIPseqPeaksHuvecCtcf     versioned
mv wgEncodeUtaChIPseqPeaksNhekCtcf      versioned
mv wgEncodeUtaChIPseqPeaksH1hescCtcf    versioned
mv wgEncodeUtaChIPseqPeaksGm12891Ctcf   versioned
mv wgEncodeUtaChIPseqPeaksGm12892Ctcf   versioned
mv wgEncodeUtaChIPseqPeaksGm19238Ctcf   versioned
mv wgEncodeUtaChIPseqPeaksGm19239Ctcf   versioned
mv wgEncodeUtaChIPseqPeaksGm19240Ctcf   versioned
mv wgEncodeUtaChIPseqPeaksGm12878Cmyc   versioned
mv wgEncodeUtaChIPseqPeaksHuvecCmyc     versioned
mv wgEncodeUtaChIPseqPeaksK562Pol2      versioned
mv wgEncodeUtaChIPseqPeaksHepg2Pol2     versioned
mv wgEncodeUtaChIPseqPeaksHuvecPol2     versioned
mv wgEncodeUtaChIPseqPeaksH1hescPol2    versioned
mv wgEncodeUtaChIPseqPeaksGm12878CtcfV2 versioned
mv wgEncodeUtaChIPseqPeaksK562CtcfV2    versioned
mv wgEncodeUtaChIPseqPeaksHepg2CtcfV2   versioned
mv wgEncodeUtaChIPseqPeaksHelas3CtcfV2  versioned
mv wgEncodeUtaChIPseqPeaksK562CmycV2    versioned
mv wgEncodeUtaChIPseqPeaksHepg2CmycV2   versioned
mv wgEncodeUtaChIPseqPeaksHelas3CmycV2  versioned


## No need: all are peaks: grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1097/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .

update projects set user_id = 17 where id in (1097,1098,1099,1100,1101,1102);
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1097 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1098 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1099 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1100 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1101 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1102 displayed

## Finishing up freeze:
/cluster/data/encode/pipeline/bin/encodeStatus.pl 829 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 831 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 834 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 835 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 836 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 847 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 848 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 849 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 850 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 851 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 852 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 855 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 856 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 857 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 858 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 859 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 866 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 868 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 871 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 873 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 874 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 877 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 881 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 882 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 883 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 884 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 885 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 886 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 939 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 940 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 953 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 955 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 960 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 969 approved

/cluster/data/encode/pipeline/bin/encodeStatus.pl 1097 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1098 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1099 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1100 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1101 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1102 approved

# 2010-02-09 Clean up old peaks files from downloads dir.
ll wgEncodeDukeDNaseSeqPeaksGm12878V2.narrowPeak.gz     wgEncodeDukeDNaseSeqPeaksGm12878V3.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksGm12891.narrowPeak.gz       wgEncodeDukeDNaseSeqPeaksGm12891V2.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksGm12892.narrowPeak.gz       wgEncodeDukeDNaseSeqPeaksGm12892V2.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksGm19238.narrowPeak.gz       wgEncodeDukeDNaseSeqPeaksGm19238V2.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksGm19239.narrowPeak.gz       wgEncodeDukeDNaseSeqPeaksGm19239V2.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksGm19240.narrowPeak.gz       wgEncodeDukeDNaseSeqPeaksGm19240V2.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksH1hesc.narrowPeak.gz        wgEncodeDukeDNaseSeqPeaksH1hescV2.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksHelas3V2.narrowPeak.gz      wgEncodeDukeDNaseSeqPeaksHelas3V3.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksHepg2V2.narrowPeak.gz       wgEncodeDukeDNaseSeqPeaksHepg2V3.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksHuvec.narrowPeak.gz         wgEncodeDukeDNaseSeqPeaksHuvecV2.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksK562V2.narrowPeak.gz        wgEncodeDukeDNaseSeqPeaksK562V3.narrowPeak.gz
ll wgEncodeDukeDNaseSeqPeaksNhek.narrowPeak.gz          wgEncodeDukeDNaseSeqPeaksNhekV2.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksGm12878V2.narrowPeak.gz      wgEncodeUncFAIREseqPeaksGm12878V3.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksH1hesc.narrowPeak.gz         wgEncodeUncFAIREseqPeaksH1hescV2.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksHelas3V2.narrowPeak.gz       wgEncodeUncFAIREseqPeaksHelas3V3.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksHepg2V2.narrowPeak.gz        wgEncodeUncFAIREseqPeaksHepg2V3.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksHuvec.narrowPeak.gz          wgEncodeUncFAIREseqPeaksHuvecV2.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksK562V2.narrowPeak.gz         wgEncodeUncFAIREseqPeaksK562V3.narrowPeak.gz
ll wgEncodeUncFAIREseqPeaksNhek.narrowPeak.gz           wgEncodeUncFAIREseqPeaksNhekV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksGm12878Cmyc.narrowPeak.gz     wgEncodeUtaChIPseqPeaksGm12878CmycV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksGm12878CtcfV2.narrowPeak.gz   wgEncodeUtaChIPseqPeaksGm12878CtcfV3.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksGm12891Ctcf.narrowPeak.gz     wgEncodeUtaChIPseqPeaksGm12891CtcfV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksGm12892Ctcf.narrowPeak.gz     wgEncodeUtaChIPseqPeaksGm12892CtcfV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksGm19238Ctcf.narrowPeak.gz     wgEncodeUtaChIPseqPeaksGm19238CtcfV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksGm19239Ctcf.narrowPeak.gz     wgEncodeUtaChIPseqPeaksGm19239CtcfV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksGm19240Ctcf.narrowPeak.gz     wgEncodeUtaChIPseqPeaksGm19240CtcfV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksH1hescCtcf.narrowPeak.gz      wgEncodeUtaChIPseqPeaksH1hescCtcfV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksH1hescPol2.narrowPeak.gz      wgEncodeUtaChIPseqPeaksH1hescPol2V2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksHelas3CmycV2.narrowPeak.gz    wgEncodeUtaChIPseqPeaksHelas3CmycV3.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksHelas3CtcfV2.narrowPeak.gz    wgEncodeUtaChIPseqPeaksHelas3CtcfV3.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksHepg2CmycV2.narrowPeak.gz     wgEncodeUtaChIPseqPeaksHepg2CmycV3.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksHepg2CtcfV2.narrowPeak.gz     wgEncodeUtaChIPseqPeaksHepg2CtcfV3.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksHepg2Pol2.narrowPeak.gz       wgEncodeUtaChIPseqPeaksHepg2Pol2V2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksHuvecCmyc.narrowPeak.gz       wgEncodeUtaChIPseqPeaksHuvecCmycV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksHuvecCtcf.narrowPeak.gz       wgEncodeUtaChIPseqPeaksHuvecCtcfV2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksHuvecPol2.narrowPeak.gz       wgEncodeUtaChIPseqPeaksHuvecPol2V2.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksK562CmycV2.narrowPeak.gz      wgEncodeUtaChIPseqPeaksK562CmycV3.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksK562CtcfV2.narrowPeak.gz      wgEncodeUtaChIPseqPeaksK562CtcfV3.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksK562Pol2.narrowPeak.gz        wgEncodeUtaChIPseqPeaksK562Pol2V3.narrowPeak.gz
ll wgEncodeUtaChIPseqPeaksNhekCtcf.narrowPeak.gz        wgEncodeUtaChIPseqPeaksNhekCtcfV2.narrowPeak.gz

rm wgEncodeDukeDNaseSeqPeaksGm12878V2.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksGm12891.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksGm12892.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksGm19238.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksGm19239.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksGm19240.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksH1hesc.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksHelas3V2.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksHepg2V2.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksHuvec.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksK562V2.narrowPeak.gz
rm wgEncodeDukeDNaseSeqPeaksNhek.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksGm12878V2.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksH1hesc.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksHelas3V2.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksHepg2V2.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksHuvec.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksK562V2.narrowPeak.gz
rm wgEncodeUncFAIREseqPeaksNhek.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksGm12878Cmyc.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksGm12878CtcfV2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksGm12891Ctcf.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksGm12892Ctcf.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksGm19238Ctcf.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksGm19239Ctcf.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksGm19240Ctcf.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksH1hescCtcf.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksH1hescPol2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksHelas3CmycV2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksHelas3CtcfV2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksHepg2CmycV2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksHepg2CtcfV2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksHepg2Pol2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksHuvecCmyc.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksHuvecCtcf.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksHuvecPol2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksK562CmycV2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksK562CtcfV2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksK562Pol2.narrowPeak.gz
rm wgEncodeUtaChIPseqPeaksNhekCtcf.narrowPeak.gz

/cluster/data/encode/pipeline/bin/encodeStatus.pl  856 reviewing
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2010-03-24 Zinba Peaks
======================
make submission dir 1127
move ftp'd tar into place.
tar -xzf 001_UncFAIREseq_zinba.tgz &
# patch up some DAF/DDF
~qateam/bin/scripts/doEncodeValidate.pl . /hive/groups/encode/dcc/pipeline/encpipeline_prod/1127
# various work to use old pipline stuff supporting wgEncode naming style
~qateam/bin/scripts/doEncodeLoad.pl . /hive/groups/encode/dcc/pipeline/encpipeline_prod/1127
update projects set status = "loaded" where id= 1127;
update projects set user_id = 17 where id = 1127;
# loaded into my sandbox.  Need to discuss adding them into PushQ
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1127 displayed

cd {downloadsDir}
mv ../wgEncodeUncFAIRE/*.gz .
cd release3/
ln ../*Zinba* .
cd ..
encodeDownloadsPage.pl index.html .

Old:
/cluster/data/encode/pipeline/bin/encodeStatus.pl 857 reviewing

### had to reload because of mising NHEK
~qateam/bin/scripts/doEncodeLoad.pl . /hive/groups/encode/dcc/pipeline/encpipeline_prod/1127

2010-04-23 Standardize to setType, inputType
============================================
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap" -countObjs
Using table named 'hg18.mdb_tdreszer'.
615 objects
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq" -countObjs
250 objects

mdbPrint hg18 -vars="composite=wgEncodeChromatinMap antibody=Input" -countObjs
20 objects
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq antibody=Input" -countObjs
20 objects

## So some ChIP cell lines have input and others use a model of input
select distinct t1.val cell from mdb_tdreszer t1,mdb_tdreszer t2 where t1.obj like "wgEncodeUta%"
 and t1.obj = t2.obj
 and t1.var = "cell" and t2.var = "antibody" and t2.val = "Input"
 order by t1.val,t2.val;
+---------+
| GM12878 | 
| HUVEC   | 
| HeLa-S3 | 
| HepG2   | 
| K562    | 
| MCF-7   | 
| ProgFib | 
+---------+
7 rows in set (0.02 sec)
select distinct t3.val cell from mdb_tdreszer t3 where t3.var = "cell" and t3.obj like "wgEncodeUta%" and t3.val not in 
(select t1.val from mdb_tdreszer t1,mdb_tdreszer t2 where t1.obj like "wgEncodeUta%"
 and t1.obj = t2.obj
 and t1.var = "cell" and t2.var = "antibody" and t2.val = "Input")
 order by t3.val;
+---------+
| GM12891 | 
| GM12892 | 
| GM19238 | 
| GM19239 | 
| GM19240 | 
| H1-hESC | 
| NHEK    | 
+---------+
7 rows in set (0.27 sec)
select distinct t3.val cell from mdb_tdreszer t3 where t3.var = "cell" and t3.obj like "wgEncodeUta%";
14 rows in set (0.03 sec)

mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq antibody=Input" -var=setType -val=input
Affected 20 row(s) in hg18.mdb_tdreszer
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq antibody!=Input" -var=setType -val=exp
Affected 230 row(s) in hg18.mdb_tdreszer

mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=GM12878" -var=inputType val=GM12878/Input 
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=HUVEC  " -var=inputType val=HUVEC/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=HeLa-S3" -var=inputType val=HeLa-S3/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=HepG2  " -var=inputType val=HepG2/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=K562   " -var=inputType val=K562/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=MCF-7  " -var=inputType val=MCF-7/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=ProgFib" -var=inputType val=ProgFib/Input
Affected 32 row(s) in hg18.mdb_tdreszer
Affected 22 row(s) in hg18.mdb_tdreszer
Affected 32 row(s) in hg18.mdb_tdreszer
Affected 38 row(s) in hg18.mdb_tdreszer
Affected 40 row(s) in hg18.mdb_tdreszer
Affected 17 row(s) in hg18.mdb_tdreszer
Affected 12 row(s) in hg18.mdb_tdreszer
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq inputType=?" -countObjs
193 objects

mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=GM12891" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=GM12892" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=GM19238" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=GM19239" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=GM19240" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=H1-hESC" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq cell=NHEK   " -var=inputType val=modelled
Affected 7 row(s) in hg18.mdb_tdreszer
Affected 7 row(s) in hg18.mdb_tdreszer
Affected 7 row(s) in hg18.mdb_tdreszer
Affected 7 row(s) in hg18.mdb_tdreszer
Affected 7 row(s) in hg18.mdb_tdreszer
Affected 15 row(s) in hg18.mdb_tdreszer
Affected 7 row(s) in hg18.mdb_tdreszer
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq inputType=?" -countObjs
250 objects

## What about DNase?  What about FAIRE?
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq" -countObjs
223 objects
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq" -countObjs
142 objects

# Don't bother with these because DNase and FAIRE are always setTpe=exp !
#mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq" -var=setType -val=exp -test
#mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq" -var=setType -val=exp -test

mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=GM12878" -var=inputType val=GM12878/Input 
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=HUVEC  " -var=inputType val=HUVEC/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=HeLa-S3" -var=inputType val=HeLa-S3/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=HepG2  " -var=inputType val=HepG2/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=K562   " -var=inputType val=K562/Input

mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=MCF-7  " -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=ProgFib" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=GM12891" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=GM12892" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=GM19238" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=GM19239" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=GM19240" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=H1-hESC" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=NHEK   " -var=inputType val=modelled
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq inputType=?" -countObjs
133 objects ??? expecting 223!

mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=GM12878" -var=inputType val=GM12878/Input 
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=HUVEC  " -var=inputType val=HUVEC/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=HeLa-S3" -var=inputType val=HeLa-S3/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=HepG2  " -var=inputType val=HepG2/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=K562   " -var=inputType val=K562/Input

mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=MCF-7  " -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=ProgFib" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=GM12891" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=GM12892" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=GM19238" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=GM19239" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=GM19240" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=H1-hESC" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=NHEK   " -var=inputType val=modelled
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq inputType=?" -countObjs
109 objects ??? expecting 142!


# answer is that DNase and FAIRE both have cell types that are not in this ggroup of 14
select distinct val cell from mdb_tdreszer where obj like "wgEncodeDuke%" and var = "cell" and val not in 
("GM12878","HUVEC","HeLa-S3","HepG2","K562","MCF-7","ProgFib","GM12891","GM12892","GM19238","GM19239","GM19240","H1-hESC","NHEK");
13 rows in set (0.01 sec)
select distinct val cell from mdb_tdreszer where obj like "wgEncodeUnc%" and var = "cell" and val not in 
("GM12878","HUVEC","HeLa-S3","HepG2","K562","MCF-7","ProgFib","GM12891","GM12892","GM19238","GM19239","GM19240","H1-hESC","NHEK");
4 rows in set (0.02 sec)

# Simplest: default all then set few
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=GM12878" -var=inputType val=GM12878/Input 
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=HUVEC  " -var=inputType val=HUVEC/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=HeLa-S3" -var=inputType val=HeLa-S3/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=HepG2  " -var=inputType val=HepG2/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq cell=K562   " -var=inputType val=K562/Input
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq inputType=?" -countObjs
223 objects

mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq" -var=inputType val=modelled
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=GM12878" -var=inputType val=GM12878/Input 
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=HUVEC  " -var=inputType val=HUVEC/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=HeLa-S3" -var=inputType val=HeLa-S3/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=HepG2  " -var=inputType val=HepG2/Input
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq cell=K562   " -var=inputType val=K562/Input
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq inputType=?" -countObjs
142 objects

mdbPrint hg18 -vars="composite=wgEncodeChromatinMap" > mdbOpenChrom.ra
Using table named 'hg18.mdb_tdreszer'.
objects:615  vars:10908
mdbUpdate hg18 -table=mdb mdbOpenChrom.ra -force
Read 615 metadata objects from hg18
Affected 865 row(s) in hg18.mdb
### Note that mdbOpenChrom contqains something that violates the magic.  Something that is treated differently if it is read from the mdb as opposed to read from a file?

cvs ci -m "Extended setType and inputType to Open Chromatin" mdbOpenChrom.ra

cd {downloadsDir}ChromatinMap
encodeDownloadsPage.pl -mdb=mdb index.html .

### Tests to find offending string offending magic
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=FAIREseq" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
Update to shared table 'mdb' requires file directly written by mdbPrint from sandbox file.
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=DNaseSeq" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
Update to shared table 'mdb' requires file directly written by mdbPrint from sandbox file.
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap dataType=ChIPseq" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
Update to shared table 'mdb' requires file directly written by mdbPrint from sandbox file.
All three suffer!!!

mdbPrint hg18 -vars="composite=wgEncodeChromatinMap cell=GM12878" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap cell!=GM12878" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
All GM12878 suffers along with others

mdbPrint hg18 -vars="composite=wgEncodeChromatinMap cell=GM12878 view=Signal" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=Signal" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
# Signals are fine
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=Peaks" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
# Peaks are fine
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=peaksZinba" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
# Zinba Peaks are fine
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=Base_Overlap_Signal" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
# BO Signals are fine
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=RawData" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
# Raw Data is fine
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=Alignments" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
Update to shared table 'mdb' requires file directly written by mdbPrint from sandbox file.
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view!=Alignments" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
# Alignmens and ONLY Alignments fail!
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=Alignments cell=GM12878 antibody=Pol2" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=Alignments" | grep labVersion | m
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=Alignments labVersion!=%align_on_cluster%" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
mdbPrint hg18 -vars="composite=wgEncodeChromatinMap view=Alignments labVersion=%align_on_cluster%" > testOpenChrom.ra
mdbUpdate hg18 -table=mdb testOpenChrom.ra -test
# %align_on_cluster% is the cluprit
select distinct val from mdb_tdreszer where var = "labVersion" and val like "%align_on_cluster%"; 
+----------------------------------+
| val                              |
+----------------------------------+
|  align_on_cluster.pl v 1         | 
| DNaseHS, align_on_cluster.pl v 1 | 
+----------------------------------+
mdbUpdate hg18 -vars="composite=wgEncodeChromatinMap view=Alignments labVersion=%align_on_cluster%" -var=labVersion -val="align_on_cluster.pl v 1"
Using table named 'hg18.mdb_tdreszer'.
Affected 159 row(s) in hg18.mdb_tdreszer

mdbPrint hg18 -vars="composite=wgEncodeChromatinMap" > mdbOpenChrom.ra
mdbUpdate hg18 -table=mdb mdbOpenChrom.ra -test
## Problem solved!!

cvs ci -m "Fixed labVersions with leading blank that were screwing up MAGIC" mdbOpenChrom.ra

2010-05-26 Oops!  Forgot to set status
======================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1127 approved 
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1127 reviewing 
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1127 released 


2011-04-20 Experimentify
========================
cd trackDb/human/hg18/metaDb/alpha
mdbPrint hg18 -composite=%ChromatinMap -experimentify > tmp.txt
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
objects:534  vars:9169

mdbUpdate hg18 -composite=%ChromatinMap -encodeExp=std -test    
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeChromatinMap' has 79 recognizable experiments with 79 missing an expId.
   objects/experiment: min:2  max:10  mean:6.746835.
Found 533 of 534 object(s) would have their experiment ID updated.
Command would affected 533 row(s) in hg18.metaDb_tdreszer

mdbUpdate hg18 -composite=%ChromatinMap -encodeExp=std      
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeChromatinMap' has 79 recognizable experiments with 79 missing an expId.
   objects/experiment: min:2  max:10  mean:6.746835.
Affected 533 row(s) in hg18.metaDb_tdreszer

mdbUpdate hg18 -composite=%ChromatinMap -encodeExp=std -accession -test
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeChromatinMap' has 79 recognizable experiments with 0 missing an expId.
   objects/experiment: min:2  max:10  mean:6.746835.
Found 533 of 534 object(s) would have their experiment ID updated.
Command would affected 533 row(s) in hg18.metaDb_tdreszer

mdbUpdate hg18 -composite=%ChromatinMap -encodeExp=std -accession      
Using hgFixed.encodeExp
Using table named 'hg18.metaDb_tdreszer'.
Composite 'wgEncodeChromatinMap' has 79 recognizable experiments with 0 missing an expId.
   objects/experiment: min:2  max:10  mean:6.746835.
Affected 533 row(s) in hg18.metaDb_tdreszer

mdbPrint hg18 -composite=wgEncodeChromatinMap > wgEncodeChromatinMap.ra
Using table named 'hg18.metaDb_tdreszer'.
objects:534  vars:10235

gold wgEncodeChromatinMap.ra

gold, gadd, gci, gup,gpush

cd {downloads}/wgEncodeChromatinMap
encodeDownloadsPage.pl -db=hg18 index.html
