### nhgriNreBipElnitski.txt wrangler notes for all submissions

select id,name,status from projects where name like "Elnitski%";
+-----+----------------------------------+-----------+
| id  | name                             | status    |
+-----+----------------------------------+-----------+
| 100 | Elnitski Silencer-EB-bed Nov08-6 | displayed |
| 200 | Elnitski BiP Jan09               | displayed |
| 294 | Elnitski BiP Apr09               | displayed |
+-----+----------------------------------+-----------+
3 rows in set (0.00 sec)

Elnitski Round 1
================
tar -cpzf Fake.tgz ElnitskiNRE.DAF Fake.DDF ElnitskiSilencerK562SV40.bed  
 Browse button: Invalid content_type=application/x-compressed-tar.
first line? # other junk
promoter in cv make install
promoter in encodeValidate.pl make install
missing wgEncodeNHGRINRE in trackDb.wgEncode.ra (check-in and make alpha DBS=hg18)
download dir for 'compositeTrack' is not properly configured; please contact your wrangler at: tdreszer@soe.ucsc.edu
	/usr/local/apache/htdocs/goldenPath/hg18/wgEncodeNHGRINRE

mkdir /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq
mkdir /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeDukeDnase
mv /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeNHGRINRE /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeNhgriNre

Elnitski 11/15
==============
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/100 > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/100 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/100 > upload_error 2>&1 &

Elnitski BiP 2009-01-26
=======================
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x . > validate_error 2>&1
~/bin/scripts/doEncodeValidate.pl -allowReloads x . > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x . > validate_error 2>&1
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x . > load_error 2>&1 &
~/bin/scripts/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/200 > load_error 2>&1 &

        my @cmds = ($catCmd, "egrep -v '^track|browser'", "/cluster/bin/x86_64/hgLoadBed $assembly $tableName stdin -tmpDir=$tempDir");
hgLoadBed panTro2 wgEncodeNhgriBip Hg18_Chimp_Mar06Ensembl.txt
	Reading Hg18_Chimp_Mar06Ensembl.txt
	Loaded 519 elements of size 8
	Sorted
	Creating table definition for wgEncodeNhgriBip
	Saving bed.tab
	Loading panTro2 
hgLoadBed bosTau4 wgEncodeNhgriBip Hg18_Cow_Oct07Ensembl.txt 
	Reading Hg18_Cow_Oct07Ensembl.txt
	Loaded 366 elements of size 8
	Sorted
	Creating table definition for wgEncodeNhgriBip
	Saving bed.tab
	Loading bosTau4
hgLoadBed mm9 wgEncodeNhgriBip Hg18_MM9_July07Ensembl.txt 
	Reading Hg18_MM9_July07Ensembl.txt
	Loaded 586 elements of size 8
	Sorted
	Creating table definition for wgEncodeNhgriBip
	Saving bed.tab
	Loading mm9
hgLoadBed rn4 wgEncodeNhgriBip Hg18_Rat_Nov04Ensembl.txt 
	Reading Hg18_Rat_Nov04Ensembl.txt
	Loaded 298 elements of size 8
	Sorted
	Creating table definition for wgEncodeNhgriBip
	Saving bed.tab
	Loading rn4
hgLoadBed rheMac2 wgEncodeNhgriBip Hg18_Rhesus_Jan06Ensembl.txt 
	Reading Hg18_Rhesus_Jan06Ensembl.txt
	Loaded 385 elements of size 8
	Sorted
	Creating table definition for wgEncodeNhgriBip
	Saving bed.tab
	Loading rheMac2
hgLoadBed canFam2 wgEncodeNhgriBip Hg18_Dog_May05Ensembl.txt 
	Reading Hg18_Dog_May05Ensembl.txt
	Loaded 207 elements of size 8
	Sorted
	Creating table definition for wgEncodeNhgriBip
	Saving bed.tab
	Loading canFam2
Could be simply wgEncodeNhgriBip in every DB (ie: panTro2.wgEncodeNhgriBip) Then simply need a table in each the tells what is available.
Hg18_Chimp_Mar06Ensembl.txt     Comparative     Reference_Genome        panTro2
Hg18_Cow_Oct07Ensembl.txt       Comparative     Reference_Genome        bosTau4
Hg18_MM9_July07Ensembl.txt      Comparative     Reference_Genome        mm9
Hg18_Rat_Nov04Ensembl.txt       Comparative     Reference_Genome        rn4
Hg18_Rhesus_Jan06Ensembl.txt    Comparative     Reference_Genome        rheMac2
Hg18_Dog_May05Ensembl.txt       Comparative     Reference_Genome        canFam2

select hg18.wgEncodeNhgriBip.name,hg18.wgEncodeNhgriBip.chrom,hg18.wgEncodeNhgriBip.chromStart,hg18.wgEncodeNhgriBip.chromEnd 
 from hg18.wgEncodeNhgriBip,
      panTro2.wgEncodeNhgriBip,
      rheMac2.wgEncodeNhgriBip,
      mm9.wgEncodeNhgriBip,
      rn4.wgEncodeNhgriBip,
      canFam2.wgEncodeNhgriBip,
      bosTau4.wgEncodeNhgriBip 
where hg18.wgEncodeNhgriBip.name = panTro2.wgEncodeNhgriBip.name 
  and hg18.wgEncodeNhgriBip.name = rheMac2.wgEncodeNhgriBip.name 
  and hg18.wgEncodeNhgriBip.name = mm9.wgEncodeNhgriBip.name 
  and hg18.wgEncodeNhgriBip.name = rn4.wgEncodeNhgriBip.name 
  and hg18.wgEncodeNhgriBip.name = canFam2.wgEncodeNhgriBip.name 
  and hg18.wgEncodeNhgriBip.name = bosTau4.wgEncodeNhgriBip.name limit 2;
+-----------------+-------+------------+----------+
| name            | chrom | chromStart | chromEnd |
+-----------------+-------+------------+----------+
| TMEM112B:NCAPH2 | chr22 |   49288245 | 49308779 |
| PHF5A:ACO2      | chr22 |   40185666 | 40254939 |
+-----------------+-------+------------+----------+
2 rows in set (0.00 sec)

Elnitski 2009-04-27
===================
Just loaded the hg18 BiPs again, so renamed the tables 
rename table wgEncodeNhgriBip to wgEncodeNhgriBipOld;
rename table wgEncodeNhgriBiPPromotersReferencegenomeHg18 to wgEncodeNhgriBip;

And the files in the downloads dir:
cd wgEncodeNhgriBip
mv wgEncodeNhgriBip.hg18.bed8.gz wgEncodeNhgriBip.hg18.bed8.gz.old
mv ../wgEncodeNhgriBiP/wgEncodeNhgriBiPPromotersReferencegenomeHg18.bed8.gz wgEncodeNhgriBip.hg18.bed8.gz
rm -rf wgEncodeNhgriBiP

/cluster/data/encode/pipeline/bin/encodeStatus.pl 294 displayed

/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x ../298

Redo old NREs in order to remove non-text in names 2009-07-17
=============================================================
cd 100
cp ElnitskiEBK562gamma.bed ElnitskiEBK562gamma_corrected.bed
cp ElnitskiSilencerK562gamma.bed ElnitskiSilencerK562gamma_corrected.bed
edit to replace non-UTF8 characters
rename table wgEncodeNhgriNRESilencersK562Ggamma to wgEncodeNhgriNRESilencersK562Ggamma_old;
rename table wgEncodeNhgriNREEnhancerBlockersK562Ggamma to wgEncodeNhgriNREEnhancerBlockersK562Ggamma_old;
/cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -allowReloads x ../100 > validate_error 2>&1 &
/cluster/data/encode/pipeline/bin/doEncodeLoad.pl x ../100 > load_error 2>&1 &
rename table wgEncodeNhgriNRESilencersK562Ggamma_100 to wgEncodeNhgriNRESilencersK562Ggamma;
rename table wgEncodeNhgriNREEnhancerBlockersK562Ggamma_100 to wgEncodeNhgriNREEnhancerBlockersK562Ggamma;
# in downloads dir, files were loaded to wgEncodeNhgriNRE instead of the proper wgEncodeNhgriNre
# moved old fils to "old" dir
# moved new files to proper name and location
rm -rf wgEncodeNhgriNRE

# Oops, ElnitskiSilencerK562gamma_corrected.bed was not correctedf (a '-' was not actually a '-'!)...
drop table wgEncodeNhgriNRESilencersK562Ggamma;
rename table wgEncodeNhgriNRESilencersK562Ggamma_100 to wgEncodeNhgriNRESilencersK562Ggamma;
drop table wgEncodeNhgriNREEnhancerBlockersK562Ggamma_100;

/cluster/data/encode/pipeline/bin/encodeStatus.pl 100 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl 100 reviewing

Released:
=========
/cluster/data/encode/pipeline/bin/encodeStatus.pl 200 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 294 released

2009-10-02 Finally get around to marking NREs as released
=========================================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl 100 released
