                                                                        validateFiles?
| 300 | UwChIPSeq-GM12873-DS8948-CTCF-rep1 apr09    | validate failed | 
| 396 | UwDnaseSeq-HeLa-S3-rep1 jun09               | loaded          | failed
| 407 | UwChIPSeq-WERI-CTCF-bothReps                | loaded          | failed
| 506 | UwDnaseSeq-H1-ES-rep1 sep09                 | loaded          | ok
| 507 | UwDnaseSeq-HL-60-rep1 sep09                 | loaded          | ok
| 515 | UwDnaseSeq-Jurkat-rep1(redo) sep09          | loaded          | ok
| 509 | UwDnaseSeq-NB4-rep1 sep09                   | loaded          | ok
| 510 | UwDnaseSeq-NHEK-rep1 sep09                  | loaded          | ok
| 511 | UwDnaseSeq-PANC-1-rep2 sep09                | loaded          | ok
| 512 | UwDnaseSeq-PANC-1-rep1 sep09                | loaded          | ok
| 513 | UwDnaseSeq-SAEC-rep2 sep09                  | loaded          | ok
| 514 | UwDnaseSeq-SAEC-rep1 sep09                  | loaded          | ok
| 516 | UwChIPSeq-BJ-tert-rep2-CTCF sep09           | loaded          | ok
| 517 | UwChIPSeq-BJ-tert-rep1-CTCF sep09           | loaded          | 
| 518 | UwChIPSeq-Caco-2-rep2-CTCF sep09            | loaded          | 
| 519 | UwChIPSeq-Caco-2-rep1-CTCF sep09            | loaded          | 
| 520 | UwChIPSeq-GM06990-rep1-CTCF sep09           | loaded          | V2
| 527 | UwChIPSeq-GM06990-rep2-CTCF (redo) sep09    | loaded          | V2
| 528 | UwChIPSeq-GM12878-rep2-CTCF (redo) sep09    | loaded          | V2
| 523 | UwChIPSeq-HRE-rep1-CTCF sep09               | loaded          | 
| 525 | UwChIPSeq-K562-rep2-CTCF sep09              | validate failed | 
| 526 | UwChIPSeq-NHEK-rep1-CTCF sep09              | loaded          | 
| 532 | UwChIPSeq-HeLa-S3-rep2-CTCF (redo) sep09    | validate failed | 
| 530 | UwExons-dataVersion2 (redo) sep09           | loaded          | V2
| 533 | UwExons  sep09                              | validate failed | 

/hive/groups/encode/dcc/pipeline/encpipeline_prod/396

validateFiles -type=tagAlign -genome=/cluster/data/hg18/hg18.2bit -printFailLines -mismatches=2 -isSort -mmCheckOneInN=100 Hela-DS10011.uniques.36.hg18.bed.gz       
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=100]: sequence (GAGAAATCTCCAAGAAACAGAGTGCTATTCCGCATA) length (36) does not match genomic coords (1 / 1 - chr1 224955 224956)
chr1    224955  224956  GAGAAATCTCCAAGAAACAGAGTGCTATTCCGCATA    1000    +
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=200]: sequence (TATGTTGTGTAGAGTTCAGGGGAGAGTGCGTTATAT) length (36) does not match genomic coords (1 / 1 - chr1 554492 554493)
chr1    554492  554493  TATGTTGTGTAGAGTTCAGGGGAGAGTGCGTTATAT    1000    -
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=300]: sequence (ACCCAAGGCACCCCTCTGACATCCGGCCTGCTCCTT) length (36) does not match genomic coords (1 / 1 - chr1 555237 555238)
chr1    555237  555238  ACCCAAGGCACCCCTCTGACATCCGGCCTGCTCCTT    1000    +
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=400]: sequence (TGGGTAATTGAGGAGTATGCTAAGATTTTGCGTAGT) length (36) does not match genomic coords (1 / 1 - chr1 555439 555440)
chr1    555439  555440  TGGGTAATTGAGGAGTATGCTAAGATTTTGCGTAGT    1000    -
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=500]: sequence (CTCATCATCCCCACCATCATAGCCTTCATCCCCCTC) length (36) does not match genomic coords (1 / 1 - chr1 555708 555709)
chr1    555708  555709  CTCATCATCCCCACCATCATAGCCTTCATCCCCCTC    1000    +
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=600]: sequence (GGAGTAGATTAGGCGCAGGTAGAAGTAGAGGTTAAG) length (36) does not match genomic coords (1 / 1 - chr1 555779 555780)
chr1    555779  555780  GGAGTAGATTAGGCGCAGGTAGAAGTAGAGGTTAAG    1000    -
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=700]: sequence (GTGGGGAGGAATGGGGTGGGTTTTGTGTGTTCAAAC) length (36) does not match genomic coords (1 / 1 - chr1 555865 555866)
chr1    555865  555866  GTGGGGAGGAATGGGGTGGGTTTTGTGTGTTCAAAC    1000    -
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=800]: sequence (AAGCCTCCTTATTCGAGCCGAACTGGGCCAGCCAGG) length (36) does not match genomic coords (1 / 1 - chr1 556415 556416)
chr1    556415  556416  AAGCCTCCTTATTCGAGCCGAACTGGGCCAGCCAGG    1000    +
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=900]: sequence (CCCCGCATAAACAACATAAGCTTCTGACTCTTACCC) length (36) does not match genomic coords (1 / 1 - chr1 556599 556600)
chr1    556599  556600  CCCCGCATAAACAACATAAGCTTCTGACTCTTACCC    1000    +
Error [file=Hela-DS10011.uniques.36.hg18.bed.gz, line=1000]: sequence (CCCCGCATAAACAACATAAGCTTCTGACTCTTACCC) length (36) does not match genomic coords (1 / 1 - chr1 556599 556600)
chr1    556599  556600  CCCCGCATAAACAACATAAGCTTCTGACTCTTACCC    1000    +
Aborting .. found 10 errors


/hive/groups/encode/dcc/pipeline/encpipeline_prod/407

validateFiles -type=tagAlign -genome=/cluster/data/hg18/hg18.2bit -printFailLines -mismatches=2 -isSort -mmCheckOneInN=100 WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=100]: sequence (CCCACCCCGCATCCCCGGGCTCGGGTT) length (27) does not match genomic coords (1 / 1 - chr1 511456 511457)
chr1    511456  511457  CCCACCCCGCATCCCCGGGCTCGGGTT     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=200]: sequence (TGCGATTTCTGATGACTAAAACCTGGC) length (27) does not match genomic coords (1 / 1 - chr1 576084 576085)
chr1    576084  576085  TGCGATTTCTGATGACTAAAACCTGGC     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=300]: sequence (GGCAAATCCACAGAAGTAGAAAGTAGA) length (27) does not match genomic coords (1 / 1 - chr1 765490 765491)
chr1    765490  765491  GGCAAATCCACAGAAGTAGAAAGTAGA     0       +
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=400]: sequence (ACCGAGGCGAGGGCAGGAGCAGGTGCA) length (27) does not match genomic coords (1 / 1 - chr1 795248 795249)
chr1    795248  795249  ACCGAGGCGAGGGCAGGAGCAGGTGCA     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=500]: sequence (GGCCGCCTCCGAACGTGGCCGCCGCCT) length (27) does not match genomic coords (1 / 1 - chr1 829939 829940)
chr1    829939  829940  GGCCGCCTCCGAACGTGGCCGCCGCCT     0       +
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=600]: sequence (CAGGCAGCAGAGCCTCGGGTCAACCGT) length (27) does not match genomic coords (1 / 1 - chr1 838190 838191)
chr1    838190  838191  CAGGCAGCAGAGCCTCGGGTCAACCGT     0       +
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=700]: sequence (GTCTTGGTCTGGGACACCTGGGCCCCA) length (27) does not match genomic coords (1 / 1 - chr1 846698 846699)
chr1    846698  846699  GTCTTGGTCTGGGACACCTGGGCCCCA     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=800]: sequence (AGGAACTCGGGTCCCCCAACTCCCTTG) length (27) does not match genomic coords (1 / 1 - chr1 857098 857099)
chr1    857098  857099  AGGAACTCGGGTCCCCCAACTCCCTTG     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=900]: sequence (GGGGAAGGTGGTGCCTGGTCAAACCAA) length (27) does not match genomic coords (1 / 1 - chr1 863917 863918)
chr1    863917  863918  GGGGAAGGTGGTGCCTGGTCAAACCAA     0       +
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=1000]: sequence (CCTGTGTGTACCTGTATGCATGCACAT) length (27) does not match genomic coords (1 / 1 - chr1 875726 875727)
chr1    875726  875727  CCTGTGTGTACCTGTATGCATGCACAT     0       -
Aborting .. found 10 errors

validateFiles -type=tagAlign -genome=/cluster/data/hg18/hg18.2bit -printFailLines -mismatches=2 -isSort -mmCheckOneInN=100 WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=100]: sequence (CCCACCCCGCATCCCCGGGCTCGGGTT) length (27) does not match genomic coords (1 / 1 - chr1 511456 511457)
chr1    511456  511457  CCCACCCCGCATCCCCGGGCTCGGGTT     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=200]: sequence (TGCGATTTCTGATGACTAAAACCTGGC) length (27) does not match genomic coords (1 / 1 - chr1 576084 576085)
chr1    576084  576085  TGCGATTTCTGATGACTAAAACCTGGC     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=300]: sequence (GGCAAATCCACAGAAGTAGAAAGTAGA) length (27) does not match genomic coords (1 / 1 - chr1 765490 765491)
chr1    765490  765491  GGCAAATCCACAGAAGTAGAAAGTAGA     0       +
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=400]: sequence (ACCGAGGCGAGGGCAGGAGCAGGTGCA) length (27) does not match genomic coords (1 / 1 - chr1 795248 795249)
chr1    795248  795249  ACCGAGGCGAGGGCAGGAGCAGGTGCA     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=500]: sequence (GGCCGCCTCCGAACGTGGCCGCCGCCT) length (27) does not match genomic coords (1 / 1 - chr1 829939 829940)
chr1    829939  829940  GGCCGCCTCCGAACGTGGCCGCCGCCT     0       +
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=600]: sequence (CAGGCAGCAGAGCCTCGGGTCAACCGT) length (27) does not match genomic coords (1 / 1 - chr1 838190 838191)
chr1    838190  838191  CAGGCAGCAGAGCCTCGGGTCAACCGT     0       +
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=700]: sequence (GTCTTGGTCTGGGACACCTGGGCCCCA) length (27) does not match genomic coords (1 / 1 - chr1 846698 846699)
chr1    846698  846699  GTCTTGGTCTGGGACACCTGGGCCCCA     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=800]: sequence (AGGAACTCGGGTCCCCCAACTCCCTTG) length (27) does not match genomic coords (1 / 1 - chr1 857098 857099)
chr1    857098  857099  AGGAACTCGGGTCCCCCAACTCCCTTG     0       -
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=900]: sequence (GGGGAAGGTGGTGCCTGGTCAAACCAA) length (27) does not match genomic coords (1 / 1 - chr1 863917 863918)
chr1    863917  863918  GGGGAAGGTGGTGCCTGGTCAAACCAA     0       +
Error [file=WERI-DS10408-CTCF-rep1.uniques.hg18.bed.gz, line=1000]: sequence (CCTGTGTGTACCTGTATGCATGCACAT) length (27) does not match genomic coords (1 / 1 - chr1 875726 875727)
chr1    875726  875727  CCTGTGTGTACCTGTATGCATGCACAT     0       -
Aborting .. found 10 errors


These are resubmissions of datasets not publicly released:
| wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf  | 
| wgEncodeUwChIPSeqPeaksHelas3Ctcf         | 
| wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf |
| wgEncodeUwChIPSeqHotspotsRep1K562Ctcf      | 
| wgEncodeUwChIPSeqPeaksK562Ctcf             | 
| wgEncodeUwChIPSeqRawSignalRep1K562Ctcf     | 
drop table wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf;
drop table wgEncodeUwChIPSeqPeaksHelas3Ctcf;
drop table wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf;

 
Ouch!!! The problem was not duplicate experiements but only duplicate Peaks
The problem directories:
| 520 | UwChIPSeq-GM06990-rep1-CTCF sep09           | loaded          | V2
| 527 | UwChIPSeq-GM06990-rep2-CTCF (redo) sep09    | loaded          | V2
| 528 | UwChIPSeq-GM12878-rep2-CTCF (redo) sep09    | loaded          | V2
| 525 | UwChIPSeq-K562-rep2-CTCF sep09              | validate failed | 
| 532 | UwChIPSeq-HeLa-S3-rep2-CTCF (redo) sep09    | validate failed | 
| 530 | UwExons-dataVersion2 (redo) sep09           | loaded          | V2

1) Unload all in pipeline

304 track wgEncodeUwChIPSeqRawSignalRep1Helas3Ctcf
    track wgEncodeUwChIPSeqPeaksHelas3Ctcf
    track wgEncodeUwChIPSeqHotspotsRep1Helas3Ctcf

2) Edit 304 daf/ddf to just reload these three tables
then submit for validation
3) Edit each of the *.dafs
4) Revalidate all the UwChipSeq tracks loaded this weekend.

# DnaseSeq look fine.
# Exon Affy look fine

### What is uwDnase HL-60/Rep2 doing as V2?? 
Unload, edit DAF, resubmit

# Tracy Ballinger did a lot of the trackDb.wgEncode.ra for DNase and ChIP.  I did for ExonAffy

/cluster/data/encode/pipeline/bin/encodeStatus.pl 530 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 534 displayed
# Tracy did the same for
506,507,509,510,511,512,513,514,514,516,517,518,519,520,523,525,526,527,528,532 
# And I redid for 304 which I had stepped on and had to reload

2009-09-30 More for the freeze
==============================
# DNase first:
| 592 | UwDnaseSeq-MCF7-7-rep1 sep09                | loaded          | 
| 625 | UwDnaseSeq-HL-60-rep1 (redo) sep09          | loaded          | 
| 627 | UwDnaseSeq-HMEC-rep1 (redo) sep09           | loaded          | 



| 595 | UwChIPSeq-Caco-2-rep1-H3K4me3 sep09         | loaded          | 
| 596 | UwChIPSeq-Caco-2-rep2-H3K4me3 sep09         | loaded          | 
| 597 | UwChIPSeq-Caco-2-rep1-H3K4me1 sep09         | loaded          | 
| 598 | UwChIPSeq-GM12878-rep1-CTCF sep09           | loaded          | 
| 599 | UwChIPSeq-HEK293-rep2-CTCF sep09            | loaded          | 
| 600 | UwChIPSeq-HMEC-rep1-H3K27me3 sep09          | loaded          | 
| 601 | UwChIPSeq-HRE-rep2-CTCF sep09               | loaded          | 
| 602 | UwChIPSeq-HRE-rep1-H3K4me1 sep09            | loaded          | 
| 603 | UwChIPSeq-HUVEC-rep1-CTCF sep09             | loaded          | 
| 604 | UwChIPSeq-HUVEC-rep1-H3K4me3 sep09          | loaded          | 
| 605 | UwChIPSeq-HUVEC-rep1-H3K27me3 sep09         | loaded          | 
| 606 | UwChIPSeq-HeLa-S3-rep1-CTCF sep09           | loaded          | 
| 607 | UwChIPSeq-HeLa-S3-rep1-H3K4me1 sep09        | loaded          | 
| 608 | UwChIPSeq-HepG2-rep2-CTCF sep09             | loaded          | 
| 609 | UwChIPSeq-HepG2-rep2-H3K4me3 sep09          | loaded          | 
| 610 | UwChIPSeq-HepG2-rep1-H3K4me3 sep09          | loaded          | 
| 611 | UwChIPSeq-K562-rep1-H3K4me3 sep09           | loaded          | 
| 612 | UwChIPSeq-NHEK-rep1-H3K4me3 sep09           | loaded          | 
| 613 | UwChIPSeq-NHEK-rep2-H3K36me3 sep09          | loaded          | 
| 622 | UwChIPSeq-HRE-rep1-H3K4me3 sep09            | loaded          | 
| 623 | UwChIPSeq-NHEK-rep1-H3K36me3 sep09          | loaded          | 
| 626 | UwChIPSeq-HEK293-rep1-CTCF sep09            | loaded          | 

Set up tdb.ra for ChIP and Dnase

#For DNase: Rearranged downloads dir to have release1
cd {downloadsDir}
mkdir release1
mv *.gz release1
# Because this is done post release: mv release1/*V2.*.gz .
cp fileDb.ra release1
cp index.html release1
# hard link them all here
ln release1/*.gz .

grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/592/out/fileDb.ra | grep parentTable > tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/625/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/627/out/fileDb.ra | grep parentTable >> tmp.txt
cp fileDb.ra fileDb.ra.2009-10-02
# edit fileDb for 3 new submissions:
   625 VERSIONING submission 311 (no change necessary)
encodeDownloadsPage.pl index.html

# Because this is done after release:
saved actual RR index.html to release1
compared lists of files in release1 to RR index.html list
removed files from release1 which are NOT in RR index.html

/cluster/data/encode/pipeline/bin/encodeStatus.pl 592 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 625 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 627 displayed

# Now ChIP
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/595/out/fileDb.ra | grep parentTable > tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/596/out/fileDb.ra | grep parentTable >> tmp.txt
...
cp fileDb.ra fileDb.ra.2009-10-02
# edit tmp.txt for replacing submissions: 
  598 replacing 301
  626 replaces 303
  606 replaces 304
  608 replaces partial 406
  611 replaces 308
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html
# Noticed that 603 was missing from tdb (because download file memtadata is incomplete)
# edit tdb.ra
# make alpha DBS=hg18
encodeDownloadsPage.pl index.html
# because peaks are submitted for rep2 but are not displayed in browser
ls wgEncodeUwChIPSeqPeaksRep2*.narrowPeak.gz
mv wgEncodeUwChIPSeqPeaksRep2*.narrowPeak.gz peakRep2/
encodeDownloadsPage.pl index.html

/cluster/data/encode/pipeline/bin/encodeStatus.pl 595 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 596 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 597 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 598 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 599 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 600 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 601 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 602 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 603 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 604 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 605 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 606 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 607 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 608 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 609 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 610 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 611 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 612 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 613 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 622 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 623 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 626 displayed

2009-10-12 Catch up with ChIPseq submissions
============================================
| 671 | UwChIPSeq-BJ-H3K4me3-rep2 sep09         | loaded |      21 | 
| 672 | UwChIPSeq-GM06990-H3K4me3-rep2 sep09    | loaded |      21 | 
| 673 | UwChIPSeq-GM12878-H3K4me3-rep2 sep09    | loaded |      21 | 
| 674 | UwChIPSeq-HL-60-H3K4me3-rep1 sep09      | loaded |      21 | 
| 675 | UwChIPSeq-HL-60-H3K4me3-rep2 sep09      | loaded |      21 | 
| 676 | UwChIPSeq-HMEC-CTCF-rep1 sep09          | loaded |      21 | 
| 677 | UwChIPSeq-HMEC-H3K27me3-rep1 sep09      | loaded |      21 | 
| 678 | UwChIPSeq-HUVEC-H3K27me3-rep1 sep09     | loaded |      21 | 
| 679 | UwChIPSeq-SAEC-H3K4me3-rep1 sep09       | loaded |      21 | 
| 680 | UwChIPSeq-SAEC-H3K4me3-rep2 sep09       | loaded |      21 | 
| 681 | UwChIPSeq-SAEC-H3K27me3.rep sep09       | loaded |      21 | 
| 682 | UwChIPSeq-SK-N-SH_RA-H3K4me3-rep1 sep09 | loaded |      21 | 
| 683 | UwChIPSeq-SK-N-SH_RA-H3K4me3-rep2 sep09 | loaded |      21 | 
| 684 | UwChIPSeq-HUVEC-H3K27me3-rep2 sep09     | loaded |      21 | 
# Loaded into trackDb 

| 652 | UwChIPSeq-BJ-tert-H3K4me3-rep1 sep09    | loaded |      21 | 
| 654 | UwChIPSeq-GM06990-H3K4me3-rep1 sep09    | loaded |      21 | 
| 655 | UwChIPSeq-HeLa-S3-H3K4me3-rep1 sep09    | loaded |      21 | 
| 656 | UwChIPSeq-HeLa-S3-H3K4me3-rep2 sep09    | loaded |      21 | 
| 657 | UwChIPSeq-HRE-H3K4me3-rep2 sep09        | loaded |      21 | 
| 658 | UwChIPSeq-HUVEC-H3K4me3-rep2 sep09      | loaded |      21 | 
| 659 | UwChIPSeq-K562-CTCF-rep1 sep09          | loaded |      21 | 
| 660 | UwChIPSeq-K562-H3K4me3-rep1 sep09       | loaded |      21 | 
| 661 | UwChIPSeq-NHEK-H3K4me3-rep2 sep09       | loaded |      21 | 
### Missing trackDb.ra???
# All of the DDFs are empty.  Make ddfs and resubmit

#edit trackDb.wgEncode.ra
make alpha DBS=hg18

cd {downloadsDir}
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/652/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/654/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/655/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/656/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/657/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/658/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/659/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/660/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/661/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/671/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/672/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/673/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/674/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/675/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/676/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/677/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/678/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/679/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/680/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/681/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/682/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/683/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/684/out/fileDb.ra | grep parentTable >> tmp.txt
# edit tmp.txt
cp fileDb.ra fileDb.ra.2009-10-13
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html

/cluster/data/encode/pipeline/bin/encodeStatus.pl 652 displayed
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#submission 520 replacing 298
# submission 598 replacing 301
# submission 626 replaces 303
# submission 606 replaces 304
# submission 608 replaces partial 406
# submission 677 (replacing 600)
# submission 678 (replacing 605)
# submission 659 (replaces 307)
# submission 660 (replaces 611,308)

update projects set status = "superceded" where id in (298,301,303,304,307,308,600,605,611); 
update projects set status = "revoked" where id in (597,602,607); 

2009-10-20 Clean up some signals
================================
Nightly:
hg18.wgEncodeUwDGFSignalHepg2 has 1 records with end > chromSize.
hg18.wgEncodeUwDGFSignalSknshra has 1 records with end > chromSize.

select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeUwDGFSignalHepg2 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chrM  |      16571 |    16572 | 16571 | 
select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeUwDGFSignalSknshra y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chrM  |      16571 |    16572 | 16571 | 
delete from wgEncodeUwDGFSignalHepg2 where chrom = "chrM" and chromEnd > 16571;
delete from wgEncodeUwDGFSignalSknshra where chrom = "chrM" and chromEnd > 16571;

# And now fix a tagAlign that overruns chr7
cd /hive/groups/encode/dcc/pipeline/encpipeline_prod/695/tags
gunzip NHEK-DS12396.uniques.36.hg18.bed.gz 
grep 158821425 NHEK-DS12396.uniques.36.hg18.bed
chr7    158821389       158821425       AGGGTTAGGGTTTAGGGTTAGGGTTAGGGTTAGGGG    1000    +
chr7    158821389       158821425       AGGGTTAGGGTTTAGGGTTAGGGTTAGGGTTAGGGG    1000    +
grep -v 158821425 NHEK-DS12396.uniques.36.hg18.bed > NHEK-DS12396.uniques.36.hg18.bed.new
mv NHEK-DS12396.uniques.36.hg18.bed NHEK-DS12396.uniques.36.hg18.old.bed
mv NHEK-DS12396.uniques.36.hg18.bed.new NHEK-DS12396.uniques.36.hg18.bed 
ll
gzip NHEK-DS12396.uniques.36.hg18.old.bed
gzip NHEK-DS12396.uniques.36.hg18.bed 

2009-10-21 More submissions
===========================
# ChIP: Melissa is handling
| 690 | UwChIPSeq-GM12878-DS11510-CTCF rep1        | loaded | 
| 691 | UwChIPSeq-HeLa-S3-DS11552-CTCF rep1        | loaded | 
| 692 | UwChIPSeq-HUVEC-DS11457-CTCF rep2          | loaded | 
| 693 | UwChIPSeq-HUVEC-DS12395-CTCF rep1          | loaded | 
| 694 | UwChIPSeq-NHEK-DS11556-CTCF rep2           | loaded | 
| 695 | UwChIPSeq-NHEK-DS12396-CTCF rep1           | loaded | 
| 696 | UwChIPSeq-SAEC-DS12397-CTCF rep2           | loaded | 
| 697 | UwChIPSeq-SAEC-DS12398-CTCF rep1           | loaded | 
| 698 | UwChIPSeq-SK-N-SH_RA-DS12399-CTCF rep1     | loaded | 
| 699 | UwChIPSeq-GM12878-DS11513-H3K4me3 rep1     | loaded | 
| 700 | UwChIPSeq-BJ-DS12194-H3K27me3 rep1         | loaded | 
| 701 | UwChIPSeq-Caco-2-DS12218-H3K27me3 rep2     | loaded | 
| 702 | UwChIPSeq-GM06990-DS12188-H3K27me3 rep2    | loaded | 
| 703 | UwChIPSeq-GM12878-DS12182-H3K27me3 rep1    | loaded | 
| 704 | UwChIPSeq-HepG2-DS12076-H3K27me3 rep1      | loaded | 
| 705 | UwChIPSeq-HepG2-DS12206-H3K27me3 rep2      | loaded | 
| 706 | UwChIPSeq-HRE-DS12415-H3K27me3 rep2        | loaded | 
| 707 | UwChIPSeq-K562-DS12066-H3K27me3 rep1       | loaded | 
| 708 | UwChIPSeq-K562-DS12068-H3K27me3 rep2       | loaded | 
| 709 | UwChIPSeq-NHEK-DS12078-H3K27me3 rep1       | loaded | 
| 710 | UwChIPSeq-NHEK-DS12080-H3K27me3 rep2       | loaded | 
| 711 | UwChIPSeq-SAEC-DS12245-H3K27me3 rep2       | loaded | 
| 712 | UwChIPSeq-SK-N-SH_RA-DS12212-H3K27me3 rep1 | loaded | 
| 713 | UwChIPSeq-Caco-2-DS12405-H3K36me3 rep2     | loaded | 
| 714 | UwChIPSeq-Caco-2-DS12406-H3K36me3 rep1     | loaded | 
| 715 | UwChIPSeq-HeLa-S3-DS12071-H3K36me3 rep1    | loaded | 
| 716 | UwChIPSeq-HeLa-S3-DS12201-H3K36me3 rep2    | loaded | 
| 717 | UwChIPSeq-HRE-DS12234-H3K36me3 rep1        | loaded | 
| 718 | UwChIPSeq-HRE-DS12418-H3K36me3 rep2        | loaded | 
| 719 | UwChIPSeq-HUVEC-DS12228-H3K36me3 rep1      | loaded | 
| 720 | UwChIPSeq-K562-DS12067-H3K36me3 rep1       | loaded | 
| 721 | UwChIPSeq-K562-DS12177-H3K36me3 rep2       | loaded | 
| 722 | UwChIPSeq-NHEK-DS12240-H3K36me3 rep2       | loaded | 
| 723 | UwChIPSeq-SAEC-DS12243-H3K36me3 rep1       | loaded | 
| 724 | UwChIPSeq-SAEC-DS12246-H3K36me3 rep2       | loaded | 
| 725 | UwChIPSeq-SK-N-SH_RA-DS12403-H3K36me3 rep2 | loaded | 
| 726 | UwChIPSeq-SK-N-SH_RA-DS12404-H3K36me3 rep1 | loaded | 
| 727 | UwChIPSeq-Caco-2-DS12221-H3K27me3 rep1     | loaded | 
| 728 | UwChIPSeq-GM06990-DS12191-H3K27me3 rep1    | loaded | 
| 729 | UwChIPSeq-GM12878-DS12185-H3K27me3 rep2    | loaded | 
| 730 | UwChIPSeq-SK-N-SH_RA-DS12215-H3K27me3 rep2 | loaded | 
| 731 | UwChIPSeq-HRE-DS12422-H3K27me3 rep1        | loaded | 
| 732 | UwChIPSeq-HeLa-S3-DS12072-H3K27me3 rep1    | loaded | 
| 733 | UwChIPSeq-HeLa-S3-DS12070-H3K27me3 rep2    | loaded | 
| 734 | UwChIPSeq-BJ-DS12197-H3K27me3 rep2         | loaded | 

# DNase: tim is handling.
| 735 | UwDnaseSeq-HGF-DS11752-rep1 sep09          | loaded | 
| 736 | UwDnaseSeq-HGF-DS11738-rep2 sep09          | loaded | 
| 737 | UwDnaseSeq-SK-N-SH_RA-DS8476-rep2 sep09    | loaded | 
| 738 | UwDnaseSeq-SKMC-DS11939-rep1 sep09         | loaded | 

Note: 737 had empty DDF.  Richard is resubmitting
cd {downloadsDir}
cp fileDb.ra fileDb.ra.2009-10-19
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/735/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/736/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/738/out/fileDb.ra | grep parentTable >> tmp.txt
# Note: no editing requirted on metadata
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html
/cluster/data/encode/pipeline/bin/encodeStatus.pl 735 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 736 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 738 displayed

hg18.wgEncodeUwDGFSignalTh1 has 1 records with end > chromSize.

select y.chrom,y.chromStart,y.chromEnd,c.size from wgEncodeUwDGFSignalTh1 y,chromInfo c where y.chrom = c.chrom and y.chromEnd > c.size;
| chrM  |      16571 |    16572 | 16571 | 
delete from wgEncodeUwDGFSignalTh1 where chrom = "chrM" and chromEnd > 16571;
Query OK, 1 row affected (0.09 sec)

cp fileDb.ra fileDb.ra.2009-10-22
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/737/out/fileDb.ra | grep parentTable >> tmp.txt
# Note: no editing requirted on metadata
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html
/cluster/data/encode/pipeline/bin/encodeStatus.pl 737 displayed

2009-10-27 More submissions.  Is the freeze finally closed???
=============================================================
# DNASE: 
# Added 754, 755 to trackDb
make alpha DBS=hg18
cd {downloadsDir}
cp fileDb.ra fileDb.ra.2009-10-27
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/754/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/755/out/fileDb.ra | grep parentTable >> tmp.txt
# e tmp.txt
cat tmp.txt >> fileDb.ra
# Eliminated 2 duplicate fileNames in fileDb.ra 
encodeDownloadsPage.pl index.html
/cluster/data/encode/pipeline/bin/encodeStatus.pl 754 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 755 displayed

# ChipSeq: 
# Melissa added 690-753 to trackDb
make alpha DBS=hg18
cd {downloadsDir}
cp fileDb.ra fileDb.ra.2009-10-27
rm tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/690/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/691/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/692/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/693/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/694/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/695/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/696/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/697/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/698/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/699/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/700/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/701/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/702/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/703/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/704/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/705/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/706/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/707/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/708/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/709/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/710/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/711/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/712/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/713/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/714/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/715/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/716/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/717/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/718/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/719/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/720/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/721/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/722/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/723/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/724/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/725/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/726/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/727/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/728/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/729/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/730/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/731/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/732/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/733/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/734/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/742/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/743/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/744/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/745/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/746/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/747/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/748/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/749/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/750/out/fileDb.ra | grep parentTable >> tmp.txt
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/753/out/fileDb.ra | grep parentTable >> tmp.txt
# e tmp.txt
cat tmp.txt >> fileDb.ra
# Eliminated 28 duplicate fileNames in fileDb.ra 
encodeDownloadsPage.pl index.html
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Versioned:
# submission 625 VERSIONING submission 311
# submission 755 VERSIONING submission 313 and REPLACING 738  738 marked superseded
# submission 737 VERSIONING 402
# submission 737 VERSIONING 402
### The versioned ones could be superseded when release2 goes public

Replacing:
#submission 520 replacing 298                298 marked superseded
# submission 690 replacing 598 replacing 301 301 marked superseded
#submission 699 replacing 302
# submission 677 (replacing 600)             301 marked superseded
# submission 693 replacing 603
# submission 678 (replacing 605)             301 marked superseded 
#submission 695 replacing 526
# submission 722 replacing 613
### Could be needing downloads dir update

2009-11-19 Clean up of downloads.
=================================
# No rep2 peaks so...
cd {downloadsDir}
mv *PeaksRep2*.gz peakReps/
encodeDownloadsPage.pl index.html
cp index.html release1/
cd release1/
ll *PeaksRep2*.gz  
rm *PeaksRep2*.gz  

### Richard noticed an error:
mkdir old
[hgwdev:tdreszer wgEncodeUwChIPSeq> mv wgEncodeUwChIPSeqPeaksGm12878Ctcf.narrowPeak.gz old
[hgwdev:tdreszer wgEncodeUwChIPSeq> encodeDownloadsPage.pl index.html 
[hgwdev:tdreszer wgEncodeUwChIPSeq> cp index.html release1/

2009-11-19 Update Release 1 from long ago
=========================================
/cluster/data/encode/pipeline/bin/encodeStatus.pl  48 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl  46 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl  50 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl  49 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 106 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 110 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 111 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 288 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 295 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 297 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 296 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 311 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 312 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 313 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 299 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 302 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 306 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 314 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 403 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 406 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 393 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 394 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 395 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 397 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 398 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 399 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 401 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 402 released
/cluster/data/encode/pipeline/bin/encodeStatus.pl 400 released

/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 299 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 302 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 306 approved
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 406 approved

2009-11-19 Need to be in QA
===========================
### TODO:
ChIP:
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 407 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 523 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 526 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 520 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 532 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 525 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 527 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 516 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 528 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 517 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 518 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 519 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 595 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 596 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 601 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 613 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 610 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 603 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 609 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 604 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 612 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 599 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 622 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 623 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 598 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 608 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 606 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 626 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 671 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 673 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 683 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 672 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 675 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 681 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 674 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 679 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 676 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 682 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 680 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 678 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 684 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 677 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 652 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 654 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 658 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 656 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 655 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 657 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 660 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 661 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 659 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 692 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 708 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 705 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 706 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 704 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 712 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 711 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 707 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 698 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 703 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 700 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 694 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 702 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 701 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 697 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 696 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 710 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 713 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 714 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 709 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 715 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 717 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 716 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 718 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 719 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 720 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 725 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 721 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 726 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 724 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 723 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 728 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 729 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 727 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 732 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 730 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 731 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 733 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 734 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 690 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 691 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 693 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 722 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 699 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 695 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 742 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 747 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 743 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 744 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 748 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 745 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 746 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 750 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 749 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 753 reviewing

DGF:
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 632 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 631 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force 637 reviewing


2009-12-16 Start on DNase release2
cd {downloadsDir}
mkdir release2
cd release2
ln ../*.gz .
cp ../index.html .
cp ../fileDb.ra .
### Realized problems with SK-N-SH_RA and SKMC
rm wgEncodeUwDnaseSeqAlignmentsRep2Sknshra.tagAlign.gz
rm release2/wgEncodeUwDnaseSeqAlignmentsRep2Sknshra.tagAlign.gz

rm wgEncodeUwDnaseSeqHotspotsRep2Sknshra.broadPeak.gz
rm release2/wgEncodeUwDnaseSeqHotspotsRep2Sknshra.broadPeak.gz

rm wgEncodeUwDnaseSeqPeaksRep2Sknshra.narrowPeak.gz
rm release2/wgEncodeUwDnaseSeqPeaksRep2Sknshra.narrowPeak.gz

rm wgEncodeUwDnaseSeqRawDataRep2Sknshra.fastq.gz
rm release2/wgEncodeUwDnaseSeqRawDataRep2Sknshra.fastq.gz

rm wgEncodeUwDnaseSeqRawSignalRep2Sknshra.wig.gz
rm release2/wgEncodeUwDnaseSeqRawSignalRep2Sknshra.wig.gz

rm wgEncodeUwDnaseSeqAlignmentsRep1Skmc.tagAlign.gz
rm release2/wgEncodeUwDnaseSeqAlignmentsRep1Skmc.tagAlign.gz

rm wgEncodeUwDnaseSeqHotspotsRep1Skmc.broadPeak.gz
rm release2/wgEncodeUwDnaseSeqHotspotsRep1Skmc.broadPeak.gz

rm wgEncodeUwDnaseSeqPeaksRep1Skmc.narrowPeak.gz
rm release2/wgEncodeUwDnaseSeqPeaksRep1Skmc.narrowPeak.gz

rm wgEncodeUwDnaseSeqRawDataRep1Skmc.fastq.gz
rm release2/wgEncodeUwDnaseSeqRawDataRep1Skmc.fastq.gz

rm wgEncodeUwDnaseSeqRawSignalRep1Skmc.wig.gz
rm release2/wgEncodeUwDnaseSeqRawSignalRep1Skmc.wig.gz


# use "ll *.gz" and count up the links from release1/release2
# Unchanged: count 110 (link count of 3 in release1,release2 and downloads)
wgEncodeUwDnaseSeqAlignmentsRep1Bjtert.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Caco2.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Gm06990.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Gm12878.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Helas3.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Hepg2.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Hrcepic.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Hre.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Huvec.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1K562.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Sknshra.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Th1.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Th2.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Bjtert.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Caco2.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Gm06990.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Gm12878.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Helas3.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Hepg2.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Hrcepic.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Hre.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2K562.tagAlign.gz
wgEncodeUwDnaseSeqHotspotsRep1Bjtert.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Caco2.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Gm06990.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Gm12878.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Helas3.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Hepg2.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Hrcepic.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Hre.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Huvec.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1K562.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Sknshra.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Th1.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Th2.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Bjtert.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Caco2.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Gm06990.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Gm12878.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Helas3.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Hepg2.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Hrcepic.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Hre.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2K562.broadPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Bjtert.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Caco2.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Gm06990.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Gm12878.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Helas3.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Hepg2.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Hrcepic.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Hre.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Huvec.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1K562.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Sknshra.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Th1.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Th2.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Bjtert.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Caco2.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Gm06990.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Gm12878.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Helas3.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Hepg2.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Hrcepic.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Hre.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2K562.narrowPeak.gz
wgEncodeUwDnaseSeqRawDataRep1Bjtert.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Caco2.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Gm06990.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Gm12878.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Helas3.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Hepg2.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Hrcepic.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Hre.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Huvec.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1K562.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Sknshra.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Th1.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Th2.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Bjtert.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Caco2.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Gm06990.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Gm12878.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Helas3.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Hepg2.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Hrcepic.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Hre.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2K562.fastq.gz
wgEncodeUwDnaseSeqRawSignalRep1Bjtert.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Caco2.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Gm06990.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Gm12878.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Helas3.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Hepg2.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Hrcepic.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Hre.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Huvec.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1K562.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Sknshra.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Th1.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Th2.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Bjtert.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Caco2.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Gm06990.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Gm12878.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Helas3.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Hepg2.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Hrcepic.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Hre.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2K562.wig.gz

# Dropped (replaced): count 15 (link count of 1 in release1 only)
wgEncodeUwDnaseSeqAlignmentsRep1Hl60.tagAlign.gz
wgEncodeUwDnaseSeqHotspotsRep1Hl60.broadPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Hl60.narrowPeak.gz
wgEncodeUwDnaseSeqRawDataRep1Hl60.fastq.gz
wgEncodeUwDnaseSeqRawSignalRep1Hl60.wig.gz
wgEncodeUwDnaseSeqAlignmentsRep2Sknshra.tagAlign.gz
wgEncodeUwDnaseSeqHotspotsRep2Sknshra.broadPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Sknshra.narrowPeak.gz
wgEncodeUwDnaseSeqRawDataRep2Sknshra.fastq.gz
wgEncodeUwDnaseSeqRawSignalRep2Sknshra.wig.gz
wgEncodeUwDnaseSeqAlignmentsRep1Skmc.tagAlign.gz
wgEncodeUwDnaseSeqHotspotsRep1Skmc.broadPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Skmc.narrowPeak.gz
wgEncodeUwDnaseSeqRawDataRep1Skmc.fastq.gz
wgEncodeUwDnaseSeqRawSignalRep1Skmc.wig.gz

# Versioned: 15 (link count 2 in release2 and "V2" of a release1/link 1 file)
wgEncodeUwDnaseSeqAlignmentsRep1Hl60V2.tagAlign.gz
wgEncodeUwDnaseSeqHotspotsRep1Hl60V2.broadPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Hl60V2.narrowPeak.gz
wgEncodeUwDnaseSeqRawDataRep1Hl60V2.fastq.gz
wgEncodeUwDnaseSeqRawSignalRep1Hl60V2.wig.gz
wgEncodeUwDnaseSeqAlignmentsRep2SknshraV2.tagAlign.gz
wgEncodeUwDnaseSeqHotspotsRep2SknshraV2.broadPeak.gz
wgEncodeUwDnaseSeqPeaksRep2SknshraV2.narrowPeak.gz
wgEncodeUwDnaseSeqRawDataRep2SknshraV2.fastq.gz
wgEncodeUwDnaseSeqRawSignalRep2SknshraV2.wig.gz
wgEncodeUwDnaseSeqAlignmentsRep1SkmcV2.tagAlign.gz
wgEncodeUwDnaseSeqHotspotsRep1SkmcV2.broadPeak.gz
wgEncodeUwDnaseSeqPeaksRep1SkmcV2.narrowPeak.gz
wgEncodeUwDnaseSeqRawDataRep1SkmcV2.fastq.gz
wgEncodeUwDnaseSeqRawSignalRep1SkmcV2.wig.gz

# new: 70 (link count of 2 in release 2 and also in downloads AND not "V2")
wgEncodeUwDnaseSeqAlignmentsRep1H1es.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Hgf.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Hmec.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Jurkat.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Mcf7.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Nb4.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Nhek.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Panc1.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep1Saec.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Hgf.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Hl60.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Panc1.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Saec.tagAlign.gz
wgEncodeUwDnaseSeqAlignmentsRep2Skmc.tagAlign.gz
wgEncodeUwDnaseSeqHotspotsRep1H1es.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Hgf.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Hmec.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Jurkat.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Mcf7.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Nb4.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Nhek.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Panc1.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep1Saec.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Hgf.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Hl60.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Panc1.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Saec.broadPeak.gz
wgEncodeUwDnaseSeqHotspotsRep2Skmc.broadPeak.gz
wgEncodeUwDnaseSeqPeaksRep1H1es.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Hgf.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Hmec.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Jurkat.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Mcf7.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Nb4.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Nhek.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Panc1.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep1Saec.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Hgf.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Hl60.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Panc1.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Saec.narrowPeak.gz
wgEncodeUwDnaseSeqPeaksRep2Skmc.narrowPeak.gz
wgEncodeUwDnaseSeqRawDataRep1H1es.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Hgf.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Hmec.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Jurkat.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Mcf7.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Nb4.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Nhek.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Panc1.fastq.gz
wgEncodeUwDnaseSeqRawDataRep1Saec.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Hgf.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Hl60.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Panc1.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Saec.fastq.gz
wgEncodeUwDnaseSeqRawDataRep2Skmc.fastq.gz
wgEncodeUwDnaseSeqRawSignalRep1H1es.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Hgf.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Hmec.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Jurkat.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Mcf7.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Nb4.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Nhek.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Panc1.wig.gz
wgEncodeUwDnaseSeqRawSignalRep1Saec.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Hgf.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Hl60.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Panc1.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Saec.wig.gz
wgEncodeUwDnaseSeqRawSignalRep2Skmc.wig.gz

DNase:
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  396 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  506 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  511 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  509 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  510 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  512 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  513 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  514 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  515 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  507 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  592 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  627 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  625 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  736 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  735 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  737 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  754 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl -force  755 reviewing

2010-01-12 Jan 2010 freeze work
===============================
# bunch of new cell protocols registered (provisionally, then approved)
cvs ci -m "Approved by resources working group for Stam lab" AG04449_Stam_protocol.pdf AG04450_Stam_protocol.pdf AG09319_Stam_protocol.pdf H7-hESC_Stam_protocol.pdf HAEpiC_Stam_protocol.pdf HCM_Stam_protocol.pdf HEEpiC_Stam_protocol.pdf HIPEpiC_Stam_protocol.pdf HRPEpiC_Stam_protocol.pdf NHLF_Stam_protocol.pdf 
cp AG04449_Stam_protocol.pdf /usr/local/apache/htdocs/ENCODE/protocols/cell
cp AG04450_Stam_protocol.pdf /usr/local/apache/htdocs/ENCODE/protocols/cell
cp AG09319_Stam_protocol.pdf /usr/local/apache/htdocs/ENCODE/protocols/cell
cp H7-hESC_Stam_protocol.pdf /usr/local/apache/htdocs/ENCODE/protocols/cell
cp HAEpiC_Stam_protocol.pdf  /usr/local/apache/htdocs/ENCODE/protocols/cell
cp HCM_Stam_protocol.pdf     /usr/local/apache/htdocs/ENCODE/protocols/cell
cp HEEpiC_Stam_protocol.pdf  /usr/local/apache/htdocs/ENCODE/protocols/cell
cp HIPEpiC_Stam_protocol.pdf /usr/local/apache/htdocs/ENCODE/protocols/cell
cp HRPEpiC_Stam_protocol.pdf /usr/local/apache/htdocs/ENCODE/protocols/cell
cp NHLF_Stam_protocol.pdf    /usr/local/apache/htdocs/ENCODE/protocols/cell

### Resolved G1 as new term type "phase"
# TODO:
1) unload/reload Jurkat properly
2) Clean up any erroneous Jurkat tables/files (probably not any: make sure release2/ dir isn't hard linked to bad ones.
3) Find out from Richard what prior submission should be a G1, then fix metadata
4) In trackDb, probably fold G1 into cell line dimension

# after the freeze:
select id,name,status,user_id from projects where status = "loaded" and user_id = 21 and id not in (1012) order by id;
|  515 | UwDnaseSeq-Jurkat-rep2(redo, demotion) sep09 | loaded |      21 | 
|  896 | UwDnaseSeq-AG04449-DS12319-1 jan10           | loaded |      21 | 
|  906 | UwDnaseSeq-AG04449-DS12329-2 jan10           | loaded |      21 | 
|  907 | UwDnaseSeq-AG04450-DS12255-2 jan10           | loaded |      21 | 
|  908 | UwDnaseSeq-AG04450-DS12270-1 jan10           | loaded |      21 | 
|  909 | UwDnaseSeq-AG09309-DS12352-1 jan10           | loaded |      21 | 
|  910 | UwDnaseSeq-AG09309-DS12357-2 jan10           | loaded |      21 | 
|  911 | UwDnaseSeq-AG09319-DS12286-2 jan10           | loaded |      21 | 
|  912 | UwDnaseSeq-AG09319-DS12291-1 jan10           | loaded |      21 | 
|  915 | UwDnaseSeq-AG10803-DS12374-2 jan10           | loaded |      21 | 
|  916 | UwDnaseSeq-CMK-DS12393-1 jan10               | loaded |      21 | 
|  917 | UwDnaseSeq-H7-hESC-DS11909-1 jan10           | loaded |      21 | 
|  918 | UwDnaseSeq-HAEpiC-DS12663-1 jan10            | loaded |      21 | 
|  919 | UwDnaseSeq-HAEpiC-DS12673-2 jan10            | loaded |      21 | 
|  921 | UwDnaseSeq-HCF-DS12491-2 jan10               | loaded |      21 | 
|  922 | UwDnaseSeq-HCPEpiC-DS12447-1 jan10           | loaded |      21 | 
|  923 | UwDnaseSeq-HCPEpiC-DS12457-2 jan10           | loaded |      21 | 
|  924 | UwDnaseSeq-HEEpiC-DS12768-2 jan10            | loaded |      21 | 
|  925 | UwDnaseSeq-HIPEpiC-DS12694-1 jan10           | loaded |      21 | 
|  926 | UwDnaseSeq-HNPCEpiC-DS12467-1 jan10          | loaded |      21 | 
|  927 | UwDnaseSeq-HNPCEpiC-DS12471-2 jan10          | loaded |      21 | 
|  929 | UwDnaseSeq-HRPEpiC-DS12568-2 jan10           | loaded |      21 | 
|  930 | UwDnaseSeq-HRPEpiC-DS12583-1 jan10           | loaded |      21 | 
|  931 | UwDnaseSeq-Jurkat-G1-DS12737-1 jan10         | loaded |      21 | 
|  932 | UwDnaseSeq-NB4-DS12538-2 jan10               | loaded |      21 | 
|  935 | UwDnaseSeq-AG10803-DS12384-1 jan10           | loaded |      21 | 
|  936 | UwDnaseSeq-NB4-DS12543-1 jan10               | loaded |      21 | 
|  937 | UwDnaseSeq-NHDF-neo-DS11923-1 jan10          | loaded |      21 | 
|  938 | UwDnaseSeq-NHDF-neo-DS11918-2 jan10          | loaded |      21 | 
|  944 | UwDnaseSeq-HCF-DS12501-1 jan10               | loaded |      21 | 
|  948 | UwDnaseSeq-HCM-DS12589-2 jan10               | loaded |      21 | 
|  949 | UwDnaseSeq-HCM-DS12599-1 jan10               | loaded |      21 | 
|  961 | UwDnaseSeq-GM12865-DS12436-1 jan10           | loaded |      21 | 
|  962 | UwDnaseSeq-GM12865-DS12442-2 jan10           | loaded |      21 | 
|  963 | UwDnaseSeq-HEEpiC-DS12763-1 jan10            | loaded |      21 | 
|  964 | UwDnaseSeq-HIPEpiC-DS12699-2 jan10           | loaded |      21 | 
|  965 | UwDnaseSeq-Jurkat-DS12659-1 jan10            | loaded |      21 | 
|  966 | UwDnaseSeq-MCF-7-DS12619-2 jan10             | loaded |      21 | 
|  967 | UwDnaseSeq-NHLF-DS12829-1 jan10              | loaded |      21 | 
|  968 | UwDnaseSeq-NHLF-DS12834-2 jan10              | loaded |      21 | 
|  982 | UwChIPSeq-GM12864-DS10988-CTCF-1 jan10       | loaded |      21 | 
|  983 | UwChIPSeq-GM12864-DS11499-CTCF-2 jan10       | loaded |      21 | 
|  984 | UwChIPSeq-GM12865-DS10991-CTCF-2 jan10       | loaded |      21 | 
|  985 | UwChIPSeq-GM12865-DS11502-CTCF-1 jan10       | loaded |      21 | 
|  986 | UwChIPSeq-GM12872-DS10989-CTCF-1 jan10       | loaded |      21 | 
|  987 | UwChIPSeq-GM12872-DS11500-CTCF-2 jan10       | loaded |      21 | 
|  988 | UwChIPSeq-GM12873-DS10990-CTCF-1 jan10       | loaded |      21 | 
|  989 | UwChIPSeq-GM12873-DS11501-CTCF-2 jan10       | loaded |      21 | 
|  990 | UwChIPSeq-GM12874-DS10992-CTCF-2 jan10       | loaded |      21 | 
|  991 | UwChIPSeq-GM12874-DS11503-CTCF-1 jan10       | loaded |      21 | 
|  992 | UwChIPSeq-GM12875-DS10993-CTCF-1 jan10       | loaded |      21 | 
|  993 | UwChIPSeq-GM12875-DS11899-CTCF-2 jan10       | loaded |      21 | 
| 1027 | UwDgf-K562-DS9767 jan10                      | loaded |      21 | 
| 1054 | UwDgf-GM06990-DS7748 jan10                   | loaded |      21 | 
+------+----------------------------------------------+--------+---------+
54 rows in set (0.00 sec)

# Gave UwDnaseSeq-A% and UwDnaseSeq-H% to Krish 
| 916 | UwDnaseSeq-CMK-DS12393-1 jan10               | loaded | 
| 961 | UwDnaseSeq-GM12865-DS12436-1 jan10           | loaded | 
| 962 | UwDnaseSeq-GM12865-DS12442-2 jan10           | loaded | 
| 965 | UwDnaseSeq-Jurkat-DS12659-1 jan10            | loaded | 
| 931 | UwDnaseSeq-Jurkat-G1-DS12737-1 jan10         | loaded | 
| 515 | UwDnaseSeq-Jurkat-rep2(redo, demotion) sep09 | loaded | 
| 966 | UwDnaseSeq-MCF-7-DS12619-2 jan10             | loaded | 
| 932 | UwDnaseSeq-NB4-DS12538-2 jan10               | loaded | 
| 936 | UwDnaseSeq-NB4-DS12543-1 jan10               | loaded | 
| 938 | UwDnaseSeq-NHDF-neo-DS11918-2 jan10          | loaded | 
| 937 | UwDnaseSeq-NHDF-neo-DS11923-1 jan10          | loaded | 
| 967 | UwDnaseSeq-NHLF-DS12829-1 jan10              | loaded | 
| 968 | UwDnaseSeq-NHLF-DS12834-2 jan10              | loaded | 

cd ../../916/out
cp trackDb.ra trackDbCombined.ra

cat ../../961/out/trackDb.ra >> trackDbCombined.ra
cat ../../962/out/trackDb.ra >> trackDbCombined.ra
cat ../../965/out/trackDb.ra >> trackDbCombined.ra
cat ../../931/out/trackDb.ra >> trackDbCombined.ra
cat ../../515/out/trackDb.ra >> trackDbCombined.ra
cat ../../966/out/trackDb.ra >> trackDbCombined.ra
cat ../../932/out/trackDb.ra >> trackDbCombined.ra
cat ../../936/out/trackDb.ra >> trackDbCombined.ra
cat ../../938/out/trackDb.ra >> trackDbCombined.ra
cat ../../937/out/trackDb.ra >> trackDbCombined.ra
cat ../../967/out/trackDb.ra >> trackDbCombined.ra
cat ../../968/out/trackDb.ra >> trackDbCombined.ra

cp fileDb.ra fileDbCombined.ra
cat ../../961/out/fileDb.ra >> fileDbCombined.ra
cat ../../962/out/fileDb.ra >> fileDbCombined.ra
cat ../../965/out/fileDb.ra >> fileDbCombined.ra
cat ../../931/out/fileDb.ra >> fileDbCombined.ra
cat ../../515/out/fileDb.ra >> fileDbCombined.ra
cat ../../966/out/fileDb.ra >> fileDbCombined.ra
cat ../../932/out/fileDb.ra >> fileDbCombined.ra
cat ../../936/out/fileDb.ra >> fileDbCombined.ra
cat ../../938/out/fileDb.ra >> fileDbCombined.ra
cat ../../937/out/fileDb.ra >> fileDbCombined.ra
cat ../../967/out/fileDb.ra >> fileDbCombined.ra
cat ../../968/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra

# edit for Hotspots CMK, GM12865, JurkatG1, NHDFneo, NHLF
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/916/out/trackDbCombined.ra trackDb.wgEncode.ra
# Jurkat Rep1 is duplicate, but this is expected.  Copy it to trackDbJurkat.ra

encodePatchTdb -mode=replace /hive/groups/encode/dcc/pipeline/encpipeline_prod/916/out/trackDbJurkat.ra trackDb.wgEncode.ra

cvs ci
make alpha DBS=hg18

grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/916/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .

/cluster/data/encode/pipeline/bin/encodeStatus.pl 916 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 961 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 962 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 965 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 931 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 515 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 966 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 932 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 936 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 938 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 937 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 967 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 968 displayed
# Done with 13

### Now start another 17
cd ../../917/out
cp trackDb.ra trackDbCombined.ra

cat ../../918/out/trackDb.ra >> trackDbCombined.ra
cat ../../919/out/trackDb.ra >> trackDbCombined.ra
cat ../../921/out/trackDb.ra >> trackDbCombined.ra
cat ../../944/out/trackDb.ra >> trackDbCombined.ra
cat ../../948/out/trackDb.ra >> trackDbCombined.ra
cat ../../949/out/trackDb.ra >> trackDbCombined.ra
cat ../../922/out/trackDb.ra >> trackDbCombined.ra
cat ../../923/out/trackDb.ra >> trackDbCombined.ra
cat ../../963/out/trackDb.ra >> trackDbCombined.ra
cat ../../924/out/trackDb.ra >> trackDbCombined.ra
cat ../../925/out/trackDb.ra >> trackDbCombined.ra
cat ../../964/out/trackDb.ra >> trackDbCombined.ra
cat ../../926/out/trackDb.ra >> trackDbCombined.ra
cat ../../927/out/trackDb.ra >> trackDbCombined.ra
cat ../../929/out/trackDb.ra >> trackDbCombined.ra
cat ../../930/out/trackDb.ra >> trackDbCombined.ra

cp fileDb.ra fileDbCombined.ra
cat ../../918/out/fileDb.ra >> fileDbCombined.ra
cat ../../919/out/fileDb.ra >> fileDbCombined.ra
cat ../../921/out/fileDb.ra >> fileDbCombined.ra
cat ../../944/out/fileDb.ra >> fileDbCombined.ra
cat ../../948/out/fileDb.ra >> fileDbCombined.ra
cat ../../949/out/fileDb.ra >> fileDbCombined.ra
cat ../../922/out/fileDb.ra >> fileDbCombined.ra
cat ../../923/out/fileDb.ra >> fileDbCombined.ra
cat ../../963/out/fileDb.ra >> fileDbCombined.ra
cat ../../924/out/fileDb.ra >> fileDbCombined.ra
cat ../../925/out/fileDb.ra >> fileDbCombined.ra
cat ../../964/out/fileDb.ra >> fileDbCombined.ra
cat ../../926/out/fileDb.ra >> fileDbCombined.ra
cat ../../927/out/fileDb.ra >> fileDbCombined.ra
cat ../../929/out/fileDb.ra >> fileDbCombined.ra
cat ../../930/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra

# edit for Hotspots H7es HAE,  HCF, HCM, HCPE, HEE, HIPE, HNPCE, HRPE
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/917/out/trackDbCombined.ra trackDb.wgEncode.ra

cvs ci
make alpha DBS=hg18

grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/917/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .

/cluster/data/encode/pipeline/bin/encodeStatus.pl 917 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 918 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 919 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 921 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 944 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 948 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 949 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 922 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 923 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 963 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 924 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 925 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 964 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 926 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 927 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 929 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 930 displayed
# Done with 17

### Now start final 10 for UW DNaseI
cd ../../896/out
cp trackDb.ra trackDbCombined.ra

cat ../../906/out/trackDb.ra >> trackDbCombined.ra
cat ../../907/out/trackDb.ra >> trackDbCombined.ra
cat ../../908/out/trackDb.ra >> trackDbCombined.ra
cat ../../909/out/trackDb.ra >> trackDbCombined.ra
cat ../../910/out/trackDb.ra >> trackDbCombined.ra
cat ../../911/out/trackDb.ra >> trackDbCombined.ra
cat ../../912/out/trackDb.ra >> trackDbCombined.ra
cat ../../915/out/trackDb.ra >> trackDbCombined.ra
cat ../../935/out/trackDb.ra >> trackDbCombined.ra

cp fileDb.ra fileDbCombined.ra
cat ../../906/out/fileDb.ra >> fileDbCombined.ra
cat ../../907/out/fileDb.ra >> fileDbCombined.ra
cat ../../908/out/fileDb.ra >> fileDbCombined.ra
cat ../../909/out/fileDb.ra >> fileDbCombined.ra
cat ../../910/out/fileDb.ra >> fileDbCombined.ra
cat ../../911/out/fileDb.ra >> fileDbCombined.ra
cat ../../912/out/fileDb.ra >> fileDbCombined.ra
cat ../../915/out/fileDb.ra >> fileDbCombined.ra
cat ../../935/out/fileDb.ra >> fileDbCombined.ra
e trackDbCombined.ra fileDbCombined.ra

# edit for Hotspots, AG04449, AG04450, AG09309, AG09319, AG10803  
encodePatchTdb -test=tmp.ra /hive/groups/encode/dcc/pipeline/encpipeline_prod/896/out/trackDbCombined.ra trackDb.wgEncode.ra

cvs ci
make alpha DBS=hg18

grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/896/out/fileDbCombined.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .

/cluster/data/encode/pipeline/bin/encodeStatus.pl 896 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 906 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 907 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 908 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 909 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 910 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 911 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 912 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 915 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 935 displayed

### Missing Jurkat Rep 2 !
cd {pip}/515
doEncodeLoad.pl -verbose 2 x /hive/groups/encode/dcc/pipeline/encpipeline_prod/515 &

# UW ChIP - Krish loaded up trackDb and downlaods
# UW DGF (Krish loaded up trackDb) downlaods:
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1027/out/fileDb.ra | grep parentTable >> fileDb.ra
grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1054/out/fileDb.ra | grep parentTable >> fileDb.ra
encodeDownloadsPage.pl index.html .


hg18.wgEncodeUwDGFSignalGm06990 has 1 records with end > chromSize.
hg18.wgEncodeUwDGFSignalK562 has 1 records with end > chromSize.
update wgEncodeUwDGFSignalGm06990 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;
update wgEncodeUwDGFSignalK562 y,chromInfo c set y.chromEnd = c.size where y.chrom = c.chrom and y.chromEnd > c.size;

# At the freeze:
select id,name,status,user_id,created_at from projects where status = "displayed" and name like "UWCh%" and created_at > date('2009-11-01') order by name;
+-----+----------------------------------------+-----------+---------+---------------------+
| id  | name                                   | status    | user_id | created_at          |
+-----+----------------------------------------+-----------+---------+---------------------+
| 982 | UwChIPSeq-GM12864-DS10988-CTCF-1 jan10 | displayed |      21 | 2010-01-11 15:30:31 | 
| 983 | UwChIPSeq-GM12864-DS11499-CTCF-2 jan10 | displayed |      21 | 2010-01-11 15:30:47 | 
| 984 | UwChIPSeq-GM12865-DS10991-CTCF-2 jan10 | displayed |      21 | 2010-01-11 15:31:06 | 
| 985 | UwChIPSeq-GM12865-DS11502-CTCF-1 jan10 | displayed |      21 | 2010-01-11 15:31:20 | 
| 986 | UwChIPSeq-GM12872-DS10989-CTCF-1 jan10 | displayed |      21 | 2010-01-11 15:31:32 | 
| 987 | UwChIPSeq-GM12872-DS11500-CTCF-2 jan10 | displayed |      21 | 2010-01-11 15:32:49 | 
| 988 | UwChIPSeq-GM12873-DS10990-CTCF-1 jan10 | displayed |      21 | 2010-01-11 15:33:10 | 
| 989 | UwChIPSeq-GM12873-DS11501-CTCF-2 jan10 | displayed |      21 | 2010-01-11 15:43:42 | 
| 990 | UwChIPSeq-GM12874-DS10992-CTCF-2 jan10 | displayed |      21 | 2010-01-11 15:44:05 | 
| 991 | UwChIPSeq-GM12874-DS11503-CTCF-1 jan10 | displayed |      21 | 2010-01-11 15:44:34 | 
| 992 | UwChIPSeq-GM12875-DS10993-CTCF-1 jan10 | displayed |      21 | 2010-01-11 15:44:44 | 
| 993 | UwChIPSeq-GM12875-DS11899-CTCF-2 jan10 | displayed |      21 | 2010-01-11 15:45:01 | 
+-----+----------------------------------------+-----------+---------+---------------------+
12 rows 
select id,name,status,user_id,created_at from projects where status = "displayed" and name like "UWDG%" and created_at > date('2009-11-01') order by name;
+------+----------------------------+-----------+---------+---------------------+
| id   | name                       | status    | user_id | created_at          |
+------+----------------------------+-----------+---------+---------------------+
| 1054 | UwDgf-GM06990-DS7748 jan10 | displayed |      21 | 2010-01-14 07:43:04 | 
| 1027 | UwDgf-K562-DS9767 jan10    | displayed |      21 | 2010-01-13 08:25:47 | 
+------+----------------------------+-----------+---------+---------------------+
2 rows
select id,name,status,user_id,created_at from projects where status = "displayed" and name like "UWDn%" and created_at > date('2009-11-01') order by name;
+-----+--------------------------------------+-----------+---------+---------------------+
| id  | name                                 | status    | user_id | created_at          |
+-----+--------------------------------------+-----------+---------+---------------------+
| 896 | UwDnaseSeq-AG04449-DS12319-1 jan10   | displayed |      21 | 2010-01-05 16:28:34 | 
| 906 | UwDnaseSeq-AG04449-DS12329-2 jan10   | displayed |      21 | 2010-01-07 12:37:57 | 
| 907 | UwDnaseSeq-AG04450-DS12255-2 jan10   | displayed |      21 | 2010-01-07 12:38:16 | 
| 908 | UwDnaseSeq-AG04450-DS12270-1 jan10   | displayed |      21 | 2010-01-07 12:38:33 | 
| 909 | UwDnaseSeq-AG09309-DS12352-1 jan10   | displayed |      21 | 2010-01-07 15:01:03 | 
| 910 | UwDnaseSeq-AG09309-DS12357-2 jan10   | displayed |      21 | 2010-01-07 15:01:28 | 
| 911 | UwDnaseSeq-AG09319-DS12286-2 jan10   | displayed |      21 | 2010-01-07 15:02:27 | 
| 912 | UwDnaseSeq-AG09319-DS12291-1 jan10   | displayed |      21 | 2010-01-07 15:02:44 | 
| 915 | UwDnaseSeq-AG10803-DS12374-2 jan10   | displayed |      21 | 2010-01-07 19:07:40 | 
| 935 | UwDnaseSeq-AG10803-DS12384-1 jan10   | displayed |      21 | 2010-01-08 13:41:30 | 
| 916 | UwDnaseSeq-CMK-DS12393-1 jan10       | displayed |      21 | 2010-01-07 19:08:31 | 
| 961 | UwDnaseSeq-GM12865-DS12436-1 jan10   | displayed |      21 | 2010-01-09 17:20:39 | 
| 962 | UwDnaseSeq-GM12865-DS12442-2 jan10   | displayed |      21 | 2010-01-09 17:20:55 | 
| 917 | UwDnaseSeq-H7-hESC-DS11909-1 jan10   | displayed |      21 | 2010-01-07 19:08:45 | 
| 918 | UwDnaseSeq-HAEpiC-DS12663-1 jan10    | displayed |      21 | 2010-01-07 19:09:02 | 
| 919 | UwDnaseSeq-HAEpiC-DS12673-2 jan10    | displayed |      21 | 2010-01-07 19:09:21 | 
| 921 | UwDnaseSeq-HCF-DS12491-2 jan10       | displayed |      21 | 2010-01-07 20:37:07 | 
| 944 | UwDnaseSeq-HCF-DS12501-1 jan10       | displayed |      21 | 2010-01-08 19:35:53 | 
| 948 | UwDnaseSeq-HCM-DS12589-2 jan10       | displayed |      21 | 2010-01-08 20:04:51 | 
| 949 | UwDnaseSeq-HCM-DS12599-1 jan10       | displayed |      21 | 2010-01-08 22:02:24 | 
| 922 | UwDnaseSeq-HCPEpiC-DS12447-1 jan10   | displayed |      21 | 2010-01-07 20:37:25 | 
| 923 | UwDnaseSeq-HCPEpiC-DS12457-2 jan10   | displayed |      21 | 2010-01-07 20:37:42 | 
| 963 | UwDnaseSeq-HEEpiC-DS12763-1 jan10    | displayed |      21 | 2010-01-09 17:21:36 | 
| 924 | UwDnaseSeq-HEEpiC-DS12768-2 jan10    | displayed |      21 | 2010-01-07 20:49:36 | 
| 925 | UwDnaseSeq-HIPEpiC-DS12694-1 jan10   | displayed |      21 | 2010-01-07 20:49:52 | 
| 964 | UwDnaseSeq-HIPEpiC-DS12699-2 jan10   | displayed |      21 | 2010-01-09 17:21:48 | 
| 926 | UwDnaseSeq-HNPCEpiC-DS12467-1 jan10  | displayed |      21 | 2010-01-07 22:51:38 | 
| 927 | UwDnaseSeq-HNPCEpiC-DS12471-2 jan10  | displayed |      21 | 2010-01-07 23:50:35 | 
| 929 | UwDnaseSeq-HRPEpiC-DS12568-2 jan10   | displayed |      21 | 2010-01-08 07:19:37 | 
| 930 | UwDnaseSeq-HRPEpiC-DS12583-1 jan10   | displayed |      21 | 2010-01-08 07:19:59 | 
| 965 | UwDnaseSeq-Jurkat-DS12659-1 jan10    | displayed |      21 | 2010-01-09 17:22:00 | 
| 931 | UwDnaseSeq-Jurkat-G1-DS12737-1 jan10 | displayed |      21 | 2010-01-08 07:22:17 | 
| 966 | UwDnaseSeq-MCF-7-DS12619-2 jan10     | displayed |      21 | 2010-01-09 17:22:11 | 
| 932 | UwDnaseSeq-NB4-DS12538-2 jan10       | displayed |      21 | 2010-01-08 07:24:19 | 
| 936 | UwDnaseSeq-NB4-DS12543-1 jan10       | displayed |      21 | 2010-01-08 14:08:40 | 
| 938 | UwDnaseSeq-NHDF-neo-DS11918-2 jan10  | displayed |      21 | 2010-01-08 18:27:57 | 
| 937 | UwDnaseSeq-NHDF-neo-DS11923-1 jan10  | displayed |      21 | 2010-01-08 14:34:19 | 
| 967 | UwDnaseSeq-NHLF-DS12829-1 jan10      | displayed |      21 | 2010-01-09 17:22:22 | 
| 968 | UwDnaseSeq-NHLF-DS12834-2 jan10      | displayed |      21 | 2010-01-09 17:22:44 | 
+-----+--------------------------------------+-----------+---------+---------------------+
39 rows 

NOTES for calls:
1) ChIP methods description.  In particular, text to "Display Conventions and Configuration"
2) Missing Jurkat Rep2

Issue from UW:
1) (DNase/ChIP/DGF) On the track selection page, they should put after
'Peaks" the text: '(FDR 0.5%)'.  This should also appear in the track
label for the peaks, to make it absolutely clear that these are peaks at
a very stringent FDR.
(Note that when we upgrade to HG19, we are going to convert to FDR 1%
instead of 0.5% peaks)
RESOLVED: labVersion and longLabel

2) (DNase) We need to change the cell type labels to what the cell types
actually are.  E.g., 'Pulm. Fibro.' or 'Toe Fibrol. instead of AGxyz.  
We should find out what is the character limit for this.  Then, we
should put a table below on the track description page that gives the
correspondence between the cell type names and the number codes.  We
should do this only for primary cells; leave the cell line names like
MCF7 as is.  (I am generating a table of the cell names descriptors and
send that to Tim on Monday)
PARTIALLY RESOLVED: Added to matrix title, not longLabel.  
  They will give a tighter set of "terms" and I will consider revising. 
 
3) UCSC needs to assign a color scheme (random is OK) to our cell types
that are all now black.
THEY WILL PROVIDE COLORS

4) (ChIP) Create separate sections for CTCF and Histone mod Chip-Seq data.
TO BE DONE (when other TFSB data comes in?)

5) (DNase)  GM12878 replicate order needs to be switched (rep1 -> rep2 ,
rep2 -> rep1). I'd mentioned previously that one of these samples had
been phase sorted, that is not 100% correct, so for now we'd like to
keep phasing meta-information about these blank.
RESOLVED: new metadata term "rank" and change UI labeling

6) (exon)  John has asked if it would be possible to have an alternate
signal or "wig/bedGraph" view of the exon array data (using the the
intensity value column from the data sumbitted).
BRIAN's TODO

7) (DNase)  Jurkat replicates.  It seems John has some reservations
about including sorted and unsorted replicates, we will work this out
amongst ourselves prior to the meeting I just wanted to make you aware
that there are potentially some changes for this.
RESOLVED: NO CHANGE

8) Request to break up DGF into 2 tracks: "Digital Footprinting" and "Deep Sequencing"
TO BE DONE: Will mock up both in current composite (or deep sequencing added to DNaseI)

# Edit trackDb.wgEncode.ra to add "rank" and set DNaseI GM12878 rep2 to rank 1st
make alpha DBS=hg18
cd downloads for both UW Chip and UW DNase
cp fileDb.ra fileDb.ra.2010-02-02
# edit fileDb.ra to add rank (and for DNase swap GM12878 ranks)
# add rank to encodeDownloadsPage.pl sort order
encodeDownloadsPage.pl index.html .



/cluster/data/encode/pipeline/bin/encodeStatus.pl 396 approved
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2010-02-17 Getting UW Chip back into QA
=======================================
# Problems with reset to default.  fixed in code
# Probelms with hotSpot settings.  Fixed in trackDb
# update files list "uwChIPseq.release1.notes.txt
#   create "F" category of "Added" tables and files
cd {downloadsDir}
mkdir hold
mv wgEncodeUwChIPSeqAlignmentsRep1Gm12864Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep1Gm12865Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep1Gm12872Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep1Gm12873Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep1Gm12874Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep1Gm12875Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep2Gm12864Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep2Gm12865Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep2Gm12872Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep2Gm12873Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep2Gm12874Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsRep2Gm12875Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep1Gm12864Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep1Gm12865Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep1Gm12872Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep1Gm12873Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep1Gm12874Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep1Gm12875Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep2Gm12864Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep2Gm12865Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep2Gm12872Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep2Gm12873Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep2Gm12874Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqHotspotsRep2Gm12875Ctcf.broadPeak.gz hold/
mv wgEncodeUwChIPSeqPeaksRep1Gm12864Ctcf.narrowPeak.gz hold/
mv wgEncodeUwChIPSeqPeaksRep1Gm12865Ctcf.narrowPeak.gz hold/
mv wgEncodeUwChIPSeqPeaksRep1Gm12872Ctcf.narrowPeak.gz hold/
mv wgEncodeUwChIPSeqPeaksRep1Gm12873Ctcf.narrowPeak.gz hold/
mv wgEncodeUwChIPSeqPeaksRep1Gm12874Ctcf.narrowPeak.gz hold/
mv wgEncodeUwChIPSeqPeaksRep1Gm12875Ctcf.narrowPeak.gz hold/
mv wgEncodeUwChIPSeqRawDataRep1Gm12864Ctcf.fastq.gz    hold/
mv wgEncodeUwChIPSeqRawDataRep1Gm12865Ctcf.fastq.gz    hold/
mv wgEncodeUwChIPSeqRawDataRep1Gm12872Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep1Gm12873Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep1Gm12874Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep1Gm12875Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep2Gm12864Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep2Gm12865Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep2Gm12872Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep2Gm12873Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep2Gm12874Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawDataRep2Gm12875Ctcf.fastq.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep1Gm12864Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep1Gm12865Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep1Gm12872Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep1Gm12873Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep1Gm12874Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep1Gm12875Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep2Gm12864Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep2Gm12865Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep2Gm12872Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep2Gm12873Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep2Gm12874Ctcf.wig.gz hold/
mv wgEncodeUwChIPSeqRawSignalRep2Gm12875Ctcf.wig.gz hold/

cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/982/tags/GM12864-DS10988.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep1Gm12864Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/985/tags/GM12865-DS11502.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep1Gm12865Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/986/tags/GM12872-DS10989.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep1Gm12872Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/988/tags/GM12873-DS10990.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep1Gm12873Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/991/tags/GM12874-DS11503.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep1Gm12874Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/992/tags/GM12875-DS10993.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep1Gm12875Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/983/tags/GM12864-DS11499.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep2Gm12864Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/984/tags/GM12865-DS10991.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep2Gm12865Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/987/tags/GM12872-DS11500.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep2Gm12872Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/989/tags/GM12873-DS11501.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep2Gm12873Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/990/tags/GM12874-DS10992.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep2Gm12874Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/993/tags/GM12875-DS11899.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsRep2Gm12875Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/982/hotspots/GM12864-DS10988.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep1Gm12864Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/985/hotspots/GM12865-DS11502.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep1Gm12865Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/986/hotspots/GM12872-DS10989.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep1Gm12872Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/988/hotspots/GM12873-DS10990.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep1Gm12873Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/991/hotspots/GM12874-DS11503.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep1Gm12874Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/992/hotspots/GM12875-DS10993.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep1Gm12875Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/983/hotspots/GM12864-DS11499.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep2Gm12864Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/984/hotspots/GM12865-DS10991.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep2Gm12865Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/987/hotspots/GM12872-DS11500.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep2Gm12872Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/989/hotspots/GM12873-DS11501.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep2Gm12873Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/990/hotspots/GM12874-DS10992.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep2Gm12874Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/993/hotspots/GM12875-DS11899.hotspot.twopass.merge150.wgt10.zgt2.hg18.bed.gz wgEncodeUwChIPSeqHotspotsRep2Gm12875Ctcf.broadPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/982/peaks/GM12864-DS10988.peaks.fdr.005.hg18.bed.gz wgEncodeUwChIPSeqPeaksRep1Gm12864Ctcf.narrowPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/985/peaks/GM12865-DS11502.peaks.fdr.005.hg18.bed.gz wgEncodeUwChIPSeqPeaksRep1Gm12865Ctcf.narrowPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/986/peaks/GM12872-DS10989.peaks.fdr.005.hg18.bed.gz wgEncodeUwChIPSeqPeaksRep1Gm12872Ctcf.narrowPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/988/peaks/GM12873-DS10990.peaks.fdr.005.hg18.bed.gz wgEncodeUwChIPSeqPeaksRep1Gm12873Ctcf.narrowPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/991/peaks/GM12874-DS11503.peaks.fdr.005.hg18.bed.gz wgEncodeUwChIPSeqPeaksRep1Gm12874Ctcf.narrowPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/992/peaks/GM12875-DS10993.peaks.fdr.005.hg18.bed.gz wgEncodeUwChIPSeqPeaksRep1Gm12875Ctcf.narrowPeak.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/982/fastq/GM12864-DS10988.UWStam_090608_SOLEXA-1GA-2_0006_FC427K4_2.fastq.gz wgEncodeUwChIPSeqRawDataRep1Gm12864Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/985/fastq/GM12865-DS11502.UWStam_090831_SOLEXA-1GA-1_0020_FC42KUG_3.fastq.gz wgEncodeUwChIPSeqRawDataRep1Gm12865Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/986/fastq/GM12872-DS10989.UWStam_090608_SOLEXA-1GA-2_0006_FC427K4_3.fastq.gz wgEncodeUwChIPSeqRawDataRep1Gm12872Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/988/fastq/GM12873-DS10990.UWStam_090608_SOLEXA-1GA-2_0006_FC427K4_4.fastq.gz wgEncodeUwChIPSeqRawDataRep1Gm12873Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/991/fastq/GM12874-DS11503.UWStam_090831_SOLEXA-1GA-1_0020_FC42KUG_4.fastq.gz wgEncodeUwChIPSeqRawDataRep1Gm12874Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/992/fastq/GM12875-DS10993.UWStam_090608_SOLEXA-1GA-2_0006_FC427K4_7.fastq.gz wgEncodeUwChIPSeqRawDataRep1Gm12875Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/983/fastq/GM12864-DS11499.UWStam_090810_SOLEXA-1GA-1_0013_FC42BE1_4.fastq.gz wgEncodeUwChIPSeqRawDataRep2Gm12864Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/984/fastq/GM12865-DS10991.UWStam_090608_SOLEXA-1GA-2_0006_FC427K4_5.fastq.gz wgEncodeUwChIPSeqRawDataRep2Gm12865Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/987/fastq/GM12872-DS11500.UWStam_090831_SOLEXA-1GA-1_0020_FC42KUG_1.fastq.gz wgEncodeUwChIPSeqRawDataRep2Gm12872Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/989/fastq/GM12873-DS11501.UWStam_090831_SOLEXA-1GA-1_0020_FC42KUG_2.fastq.gz wgEncodeUwChIPSeqRawDataRep2Gm12873Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/990/fastq/GM12874-DS10992.UWStam_090608_SOLEXA-1GA-2_0006_FC427K4_6.fastq.gz wgEncodeUwChIPSeqRawDataRep2Gm12874Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/993/fastq/GM12875-DS11899.UWStam_090905_SOLEXA-1GA-2_0021_FC42LOR_2.fastq.gz wgEncodeUwChIPSeqRawDataRep2Gm12875Ctcf.fastq.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/982/rawSignal/GM12864-DS10988.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep1Gm12864Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/985/rawSignal/GM12865-DS11502.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep1Gm12865Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/986/rawSignal/GM12872-DS10989.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep1Gm12872Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/988/rawSignal/GM12873-DS10990.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep1Gm12873Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/991/rawSignal/GM12874-DS11503.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep1Gm12874Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/992/rawSignal/GM12875-DS10993.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep1Gm12875Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/983/rawSignal/GM12864-DS11499.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep2Gm12864Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/984/rawSignal/GM12865-DS10991.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep2Gm12865Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/987/rawSignal/GM12872-DS11500.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep2Gm12872Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/989/rawSignal/GM12873-DS11501.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep2Gm12873Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/990/rawSignal/GM12874-DS10992.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep2Gm12874Ctcf.wig.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/993/rawSignal/GM12875-DS11899.75.20.filtered-density.36.hg18.wig.gz wgEncodeUwChIPSeqRawSignalRep2Gm12875Ctcf.wig.gz        
rm -rf hold

cd release1/
ln ../wgEncodeUwChIPSeqAlignmentsRep1Gm12864Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep1Gm12865Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep1Gm12872Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep1Gm12873Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep1Gm12874Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep1Gm12875Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep2Gm12864Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep2Gm12865Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep2Gm12872Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep2Gm12873Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep2Gm12874Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqAlignmentsRep2Gm12875Ctcf.tagAlign.gz
ln ../wgEncodeUwChIPSeqHotspotsRep1Gm12864Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep1Gm12865Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep1Gm12872Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep1Gm12873Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep1Gm12874Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep1Gm12875Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep2Gm12864Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep2Gm12865Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep2Gm12872Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep2Gm12873Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep2Gm12874Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqHotspotsRep2Gm12875Ctcf.broadPeak.gz
ln ../wgEncodeUwChIPSeqPeaksRep1Gm12864Ctcf.narrowPeak.gz
ln ../wgEncodeUwChIPSeqPeaksRep1Gm12865Ctcf.narrowPeak.gz
ln ../wgEncodeUwChIPSeqPeaksRep1Gm12872Ctcf.narrowPeak.gz
ln ../wgEncodeUwChIPSeqPeaksRep1Gm12873Ctcf.narrowPeak.gz
ln ../wgEncodeUwChIPSeqPeaksRep1Gm12874Ctcf.narrowPeak.gz
ln ../wgEncodeUwChIPSeqPeaksRep1Gm12875Ctcf.narrowPeak.gz
ln ../wgEncodeUwChIPSeqRawDataRep1Gm12864Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep1Gm12865Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep1Gm12872Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep1Gm12873Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep1Gm12874Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep1Gm12875Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep2Gm12864Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep2Gm12865Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep2Gm12872Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep2Gm12873Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep2Gm12874Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawDataRep2Gm12875Ctcf.fastq.gz
ln ../wgEncodeUwChIPSeqRawSignalRep1Gm12864Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep1Gm12865Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep1Gm12872Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep1Gm12873Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep1Gm12874Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep1Gm12875Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep2Gm12864Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep2Gm12865Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep2Gm12872Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep2Gm12873Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep2Gm12874Ctcf.wig.gz
ln ../wgEncodeUwChIPSeqRawSignalRep2Gm12875Ctcf.wig.gz
cp ../index.html .
cp ../files.txt . 
cp ../md5sum.txt .

### Need to figure out what is wrong with these and "gzip: stdout: Broken pipe" (possibly the same issue)
-rw-rw-r-- 2       4030 protein   91818790 Aug  7  2009 wgEncodeUwChIPSeqAlignmentsRep1Gm12801Ctcf.tagAlign.gz
-rw-rw-r-- 2       4030 protein  183393291 Aug  7  2009 wgEncodeUwChIPSeqAlignmentsRep1Hepg2Ctcf.tagAlign.gz
-rw-rw-r-- 2       4030 protein  146282491 Aug  7  2009 wgEncodeUwChIPSeqAlignmentsRep1Hl60Ctcf.tagAlign.gz
-rw-rw-r-- 2       4030 protein  188617281 Aug  7  2009 wgEncodeUwChIPSeqAlignmentsRep1Werirb1Ctcf.tagAlign.gz
-rw-rw-r-- 2       4030 protein  121758326 Aug  7  2009 wgEncodeUwChIPSeqAlignmentsRep2Werirb1Ctcf.tagAlign.gz

# No problem with 4030s  
# No problem with gzip errors: this is a side affect of validateFiles finding errors then jumping out beofre full zcat

### The Inputs have finally arrived: sibId=1107
mkdir hold/
mv wgEncodeUwChIPSeqAlignmentsK562Ctcf.tagAlign.gz    hold/
mv wgEncodeUwChIPSeqAlignmentsGm12801Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsHelas3Ctcf.tagAlign.gz  hold/
mv wgEncodeUwChIPSeqAlignmentsHepg2Ctcf.tagAlign.gz   hold/
mv wgEncodeUwChIPSeqAlignmentsSknshraCtcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsGm12872Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsGm12873Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsGm12864Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsHl60Ctcf.tagAlign.gz    hold/
mv wgEncodeUwChIPSeqAlignmentsHmecCtcf.tagAlign.gz    hold/
mv wgEncodeUwChIPSeqAlignmentsWerirb1Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsGm12874Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsGm12865Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsCaco2Ctcf.tagAlign.gz   hold/
mv wgEncodeUwChIPSeqAlignmentsHreCtcf.tagAlign.gz     hold/
mv wgEncodeUwChIPSeqAlignmentsGm12875Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsSaecCtcf.tagAlign.gz    hold/
mv wgEncodeUwChIPSeqAlignmentsGm12878Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsHuvecCtcf.tagAlign.gz   hold/
mv wgEncodeUwChIPSeqAlignmentsGm06990Ctcf.tagAlign.gz hold/
mv wgEncodeUwChIPSeqAlignmentsNhekCtcf.tagAlign.gz    hold/
mv wgEncodeUwChIPSeqAlignmentsBjCtcf.tagAlign.gz      hold/
mv wgEncodeUwChIPSeqAlignmentsHek293Ctcf.tagAlign.gz  hold/

cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/K562-DS11488.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsK562Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM12801-DS13665.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm12801Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/Hela-DS11540.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsHelas3Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/HepG2-DS13599.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsHepg2Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/SKNSH-DS11605.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsSknshraCtcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM12872-DS13585.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm12872Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM12873-DS13586.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm12873Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM12864-DS13587.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm12864Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/HL60-DS13664.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsHl60Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/HMEC-DS13600.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsHmecCtcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/WERI-DS11888.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsWerirb1Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM12874-DS13588.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm12874Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM12865-DS13590.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm12865Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/CACO2-DS13597.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsCaco2Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/HRE-DS11549.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsHreCtcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM12875-DS13589.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm12875Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/SAEC-DS11550.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsSaecCtcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM12878-DS11883.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm12878Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/HUVEC-DS11470.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsHuvecCtcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/GM06990-DS11497.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsGm06990Ctcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/NHEK-DS11542.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsNhekCtcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/BJ-DS11544.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsBjCtcf.tagAlign.gz
cp /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/tags/HEK293T-DS13603.uniques.36.hg18.bed.gz wgEncodeUwChIPSeqAlignmentsHek293Ctcf.tagAlign.gz

# Oops!  The ddf said ctcf but this is input!
mv wgEncodeUwChIPSeqAlignmentsK562Ctcf.tagAlign.gz     wgEncodeUwChIPSeqAlignmentsK562Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm12801Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm12801Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsHelas3Ctcf.tagAlign.gz   wgEncodeUwChIPSeqAlignmentsHelas3Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsHepg2Ctcf.tagAlign.gz    wgEncodeUwChIPSeqAlignmentsHepg2Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsSknshraCtcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsSknshraInput.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm12872Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm12872Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm12873Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm12873Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm12864Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm12864Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsHl60Ctcf.tagAlign.gz     wgEncodeUwChIPSeqAlignmentsHl60Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsHmecCtcf.tagAlign.gz     wgEncodeUwChIPSeqAlignmentsHmecInput.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsWerirb1Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsWerirb1Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm12874Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm12874Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm12865Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm12865Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsCaco2Ctcf.tagAlign.gz    wgEncodeUwChIPSeqAlignmentsCaco2Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsHreCtcf.tagAlign.gz      wgEncodeUwChIPSeqAlignmentsHreInput.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm12875Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm12875Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsSaecCtcf.tagAlign.gz     wgEncodeUwChIPSeqAlignmentsSaecInput.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm12878Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm12878Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsHuvecCtcf.tagAlign.gz    wgEncodeUwChIPSeqAlignmentsHuvecInput.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsGm06990Ctcf.tagAlign.gz  wgEncodeUwChIPSeqAlignmentsGm06990Input.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsNhekCtcf.tagAlign.gz     wgEncodeUwChIPSeqAlignmentsNhekInput.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsBjCtcf.tagAlign.gz       wgEncodeUwChIPSeqAlignmentsBjInput.tagAlign.gz
mv wgEncodeUwChIPSeqAlignmentsHek293Ctcf.tagAlign.gz   wgEncodeUwChIPSeqAlignmentsHek293Input.tagAlign.gz

cd release1
ln ../wgEncodeUwChIPSeqAlignmentsK562Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm12801Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsHelas3Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsHepg2Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsSknshraInput.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm12872Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm12873Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm12864Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsHl60Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsHmecInput.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsWerirb1Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm12874Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm12865Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsCaco2Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsHreInput.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm12875Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsSaecInput.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm12878Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsHuvecInput.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsGm06990Input.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsNhekInput.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsBjInput.tagAlign.gz .
ln ../wgEncodeUwChIPSeqAlignmentsHek293Input.tagAlign.gz .
cd ..

grep metadata /hive/groups/encode/dcc/pipeline/encpipeline_prod/1107/out/fileDb.ra | grep parentTable > tmp.txt
cat tmp.txt >> fileDb.ra
encodeDownloadsPage.pl index.html
encodeDownloadsPage.pl -checksum index.html . &
cp index.html release1/
cp fileDb.ra release1/
cp files.txt release1/
cp md5sum.txt release1/
cp preamble.html release1/

/cluster/data/encode/pipeline/bin/encodeStatus.pl 1107 displayed
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1107 approved

/cluster/data/encode/pipeline/bin/encodeStatus.pl 982 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 983 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 984 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 985 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 986 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 987 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 988 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 989 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 990 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 991 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 992 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 993 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 1107 reviewing

2010-02-19 Getting ready for UW DNase release 3
===============================================
Edit trackDb.wgEncode.ra and wgEncodeUwDnaseSeq.html for release notes, versioning and dataVersion
cd {downloadsDir}
mkdir release3
cp index.html release3
cp preamble.html release3
cp fileDb.ra release3
cp files.txt release3
cp md5sum.txt release3
cd release3/
ln ../*.gz .

### NOTE: spent time fixing all the symlinks which had propgated to release1 and release 2 directories

Make uwDnaseSeq.release3.notes.txt
Make pushQ entry covering 114 new tables, 191 new files and 38 new wibs; plus 3 versioned tables, 5 versioned files and 1 versioned wib

/cluster/data/encode/pipeline/bin/encodeStatus.pl 915 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 916 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 917 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 918 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 919 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 921 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 922 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 923 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 924 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 925 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 926 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 927 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 929 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 930 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 931 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 932 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 935 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 936 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 937 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 938 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 944 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 948 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 949 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 961 reviewing
/cluster/data/encode/pipeline/bin/encodeStatus.pl 962 reviewing
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2010-04-22 Move metadata to mdb!
================================
cd {hg18}
grep metadata trackDb.wgEncode.ra | grep wgEncodeUwChIPSeq  > testing/mdbUwHist.txt
wl testing/mdbUwHist.txt 340
grep -v "\#metadata" testing/mdbUwHist.txt > testing/mdbUwHist2.txt 
mv testing/mdbUwHist2.txt testing/mdbUwHist.txte
wl testing/mdbUwHist.txt 293 
mdbUpdate hg18 testing/mdbUwHist.txt
Using table named 'hg18.mdb_tdreszer'.
Read 293 metadata objects from hg18
Affected 5597 row(s) in hg18.mdb_tdreszer
cd {downlaodsDir}
mdbUpdate hg18 fileDb.ra
Using table named 'hg18.mdb_tdreszer'.
The same variable appears twice: dateUnrestricted=2010-07-11 and dateUnrestricted=2010-06-29.  Ignoring second value.
        project=wgEncode grant=Stam lab=Uw dataType=ChIPSeq cell=BJ antibody=H3K4me3 fragLength=350 view=Alignments rank=2nd replicate=2 labVersion="Eland (GAPipeline-1.4)" dataVersion="ENCODE Sep 2009 Freeze" subId=671 dateSubmitted=2009-10-12 dateUnrestricted=2010-07-11 dateUnrestricted=2010-06-29 composite=wgEncodeUwChIPSeq parentTable=wgEncodeUwChIPSeqRawSignalRep2BjH3k4me3 fileName=wgEncodeUwChIPSeqAlignmentsRep2BjH3k4me3.tagAlign.gz
Read 298 metadata objects from hg18
Affected 4994 row(s) in hg18.mdb_tdreszer
cd {hg18}
mdbPrint hg18 -vars="composite=wgEncodeUwChIPSeq" -ra > testing/mdbUwHist.ra
Using table named 'hg18.mdb_tdreszer'.
objects:561  vars:10551
mdbUpdate hg18 -table=mdb testing/mdbUwHist.ra
Read 561 metadata objects from hg18
Affected 10551 row(s) in hg18.mdb
cp testing/mdbUwHist.ra .
cvs add mdbUwHist.ra
cvs ci -m "Adding Uw Histone metadata into mdb" mdbUwHist.ra

# UW DNase
grep metadata trackDb.wgEncode.ra | grep wgEncodeUwDnaseSeq > testing/mdbUwDnase.txt
wl testing/mdbUwDnase.txt 234
grep -v "\#metadata" testing/mdbUwDnase.txt > testing/mdbUwDnase2.txt 
mv testing/mdbUwDnase2.txt testing/mdbUwDnase.txt
wl testing/mdbUwDnase.txt 231 
mdbUpdate hg18 testing/mdbUwDnase.txt
Using table named 'hg18.mdb_tdreszer'.
Read 231 metadata objects from hg18
Affected 3960 row(s) in hg18.mdb_tdreszer
cd {downlaodsDir}
mdbUpdate hg18 fileDb.ra
Using table named 'hg18.mdb_tdreszer'.
Read 237 metadata objects from hg18
Affected 2903 row(s) in hg18.mdb_tdreszer
cd {hg18}
mdbPrint hg18 -vars="composite=wgEncodeUwDnaseSeq" -ra > testing/mdbUwDnase.ra
Using table named 'hg18.mdb_tdreszer'.
objects:402  vars:6803
mdbUpdate hg18 -table=mdb testing/mdbUwDnase.ra
Read 402 metadata objects from hg18
Affected 6803 row(s) in hg18.mdb
cp testing/mdbUwDnase.ra .
cvs add mdbUwDnase.ra
cvs ci -m "Adding Uw DNase metadata into mdb" mdbUwDnase.ra

cd {hg18}
grep metadata trackDb.wgEncode.ra | grep wgEncodeUwDGF > testing/mdbUwDgf.txt
wl testing/mdbUwDgf.txt 20
grep -v "\#metadata" testing/mdbUwDgf.txt -ra > testing/mdbUwDgf2.txt 
mv testing/mdbUwDgf2.txt testing/mdbUwDgf.txt
wl testing/mdbUwDgf.txt 20
mdbUpdate hg18 testing/mdbUwDgf.txt
Using table named 'hg18.mdb_tdreszer'.
Read 20 metadata objects from hg18
Affected 295 row(s) in hg18.mdb_tdreszer
cd {downlaodsDir}
mdbUpdate hg18 wgEncodeUwDGF/fileDb.ra
Using table named 'hg18.mdb_tdreszer'.
Read 20 metadata objects from hg18
Affected 117 row(s) in hg18.mdb_tdreszer
cd {hg18}
mdbPrint hg18 -vars="composite=wgEncodeUwDGF" -ra > testing/mdbUwDgf.ra
Using table named 'hg18.mdb_tdreszer'.
objects:28  vars:412
mdbUpdate hg18 -table=mdb testing/mdbUwDgf.ra
Read 28 metadata objects from hg18
Affected 412 row(s) in hg18.mdb
cp testing/mdbUwDgf.ra .
cvs add mdbUwDgf.ra
cvs ci -m "Adding Uw DGF metadata into mdb" mdbUwDgf.ra

2010-04-23 Standardize to setType, inputType
============================================
mdbPrint hg18 -vars="composite=wgEncodeUwChIPSeq" -countObjs
Using table named 'hg18.mdb_tdreszer'.
561 objects

mdbPrint hg18 -vars="composite=wgEncodeUwChIPSeq antibody=Input" -countObjs
23 All are objType file!!

mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq antibody=Input" -var=setType -val=input
Affected 23 row(s) in hg18.mdb_tdreszer
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq antibody!=Input" -var=setType -val=exp
Affected 538 row(s) in hg18.mdb_tdreszer

select distinct t1.val cell from mdb_tdreszer t1 where t1.obj like "wgEncodeUwCh%"
 and t1.var = "cell"
 order by t1.val;
23 rows in set (0.03 sec)

mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=BJ        " -var=inputType val=BJ/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=Caco-2    " -var=inputType val=Caco-2/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM06990   " -var=inputType val=GM06990/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM12801   " -var=inputType val=GM12801/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM12864   " -var=inputType val=GM12864/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM12865   " -var=inputType val=GM12865/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM12872   " -var=inputType val=GM12872/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM12873   " -var=inputType val=GM12873/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM12874   " -var=inputType val=GM12874/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM12875   " -var=inputType val=GM12875/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=GM12878   " -var=inputType val=GM12878/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=HEK293    " -var=inputType val=HEK293/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=HL-60     " -var=inputType val=HL-60/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=HMEC      " -var=inputType val=HMEC/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=HRE       " -var=inputType val=HRE/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=HUVEC     " -var=inputType val=HUVEC/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=HeLa-S3   " -var=inputType val=HeLa-S3/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=HepG2     " -var=inputType val=HepG2/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=K562      " -var=inputType val=K562/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=NHEK      " -var=inputType val=NHEK/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=SAEC      " -var=inputType val=SAEC/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=SK-N-SH_RA" -var=inputType val=SK-N-SH_RA/Input
mdbUpdate hg18 -vars="composite=wgEncodeUwChIPSeq cell=WERI-Rb-1 " -var=inputType val=WERI-Rb-1/Input
Affected 37 row(s) in hg18.mdb_tdreszer
Affected 39 row(s) in hg18.mdb_tdreszer
Affected 38 row(s) in hg18.mdb_tdreszer
Affected 6 row(s) in hg18.mdb_tdreszer
Affected 10 row(s) in hg18.mdb_tdreszer
Affected 10 row(s) in hg18.mdb_tdreszer
Affected 10 row(s) in hg18.mdb_tdreszer
Affected 10 row(s) in hg18.mdb_tdreszer
Affected 10 row(s) in hg18.mdb_tdreszer
Affected 10 row(s) in hg18.mdb_tdreszer
Affected 39 row(s) in hg18.mdb_tdreszer
Affected 11 row(s) in hg18.mdb_tdreszer
Affected 15 row(s) in hg18.mdb_tdreszer
Affected 11 row(s) in hg18.mdb_tdreszer
Affected 39 row(s) in hg18.mdb_tdreszer
Affected 37 row(s) in hg18.mdb_tdreszer
Affected 40 row(s) in hg18.mdb_tdreszer
Affected 33 row(s) in hg18.mdb_tdreszer
Affected 35 row(s) in hg18.mdb_tdreszer
Affected 37 row(s) in hg18.mdb_tdreszer
Affected 37 row(s) in hg18.mdb_tdreszer
Affected 37 row(s) in hg18.mdb_tdreszer
Affected 10 row(s) in hg18.mdb_tdreszer
mdbPrint hg18 -vars="composite=wgEncodeUwChIPSeq inputType=?" -countObjs
561 objects
mdbPrint hg18 -vars="composite=wgEncodeUwChIPSeq" > mdbUwHist.ra
Using table named 'hg18.mdb_tdreszer'.
objects:561  vars:11673
mdbUpdate hg18 -table=mdb mdbUwHist.ra
Read 561 metadata objects from hg18
Affected 1122 row(s) in hg18.mdb
cvs ci -m "Extended setType and inputType to UW Histone" mdbUwHist.ra
cd {downloadsDir}UwHist
encodeDownloadsPage.pl -mdb=mdb index.html .

# DNase?
mdbPrint hg18 -vars="composite=wgEncodeUwDnaseSeq" -countObjs
Using table named 'hg18.mdb_tdreszer'.
402 objects
mdbPrint hg18 -vars="composite=wgEncodeUwDnaseSeq antibody=Input" -countObjs
0 objects

# DGF?
mdbPrint hg18 -vars="composite=wgEncodeUwDGF" -countObjs
Using table named 'hg18.mdb_tdreszer'.
28 objects
mdbPrint hg18 -vars="composite=wgEncodeUwDGF antibody=Input" -countObjs
0 objects
## So done with UW: only dealing with ChIP data

