### nhgriNreBipElnitski.txt wrangler notes for all submissions select id,name,status from projects where name like "Elnitski%"; +-----+----------------------------------+-----------+ | id | name | status | +-----+----------------------------------+-----------+ | 100 | Elnitski Silencer-EB-bed Nov08-6 | displayed | | 200 | Elnitski BiP Jan09 | displayed | | 294 | Elnitski BiP Apr09 | displayed | +-----+----------------------------------+-----------+ 3 rows in set (0.00 sec) Elnitski Round 1 ================ tar -cpzf Fake.tgz ElnitskiNRE.DAF Fake.DDF ElnitskiSilencerK562SV40.bed Browse button: Invalid content_type=application/x-compressed-tar. first line? # other junk promoter in cv make install promoter in encodeValidate.pl make install missing wgEncodeNHGRINRE in trackDb.wgEncode.ra (check-in and make alpha DBS=hg18) download dir for 'compositeTrack' is not properly configured; please contact your wrangler at: tdreszer@soe.ucsc.edu /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeNHGRINRE mkdir /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeYaleChIPseq mkdir /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeDukeDnase mv /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeNHGRINRE /usr/local/apache/htdocs/goldenPath/hg18/wgEncodeNhgriNre Elnitski 11/15 ============== /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/100 > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x /cluster/data/encode/pipeline/encpipeline_prod/100 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x /cluster/data/encode/pipeline/encpipeline_prod/100 > upload_error 2>&1 & Elnitski BiP 2009-01-26 ======================= /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads -quick -skipAutoCreation x . > validate_error 2>&1 ~/bin/scripts/doEncodeValidate.pl -allowReloads x . > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -allowReloads x . > validate_error 2>&1 /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x . > load_error 2>&1 & ~/bin/scripts/doEncodeLoad.pl x /hive/groups/encode/dcc/pipeline/encpipeline_prod/200 > load_error 2>&1 & my @cmds = ($catCmd, "egrep -v '^track|browser'", "/cluster/bin/x86_64/hgLoadBed $assembly $tableName stdin -tmpDir=$tempDir"); hgLoadBed panTro2 wgEncodeNhgriBip Hg18_Chimp_Mar06Ensembl.txt Reading Hg18_Chimp_Mar06Ensembl.txt Loaded 519 elements of size 8 Sorted Creating table definition for wgEncodeNhgriBip Saving bed.tab Loading panTro2 hgLoadBed bosTau4 wgEncodeNhgriBip Hg18_Cow_Oct07Ensembl.txt Reading Hg18_Cow_Oct07Ensembl.txt Loaded 366 elements of size 8 Sorted Creating table definition for wgEncodeNhgriBip Saving bed.tab Loading bosTau4 hgLoadBed mm9 wgEncodeNhgriBip Hg18_MM9_July07Ensembl.txt Reading Hg18_MM9_July07Ensembl.txt Loaded 586 elements of size 8 Sorted Creating table definition for wgEncodeNhgriBip Saving bed.tab Loading mm9 hgLoadBed rn4 wgEncodeNhgriBip Hg18_Rat_Nov04Ensembl.txt Reading Hg18_Rat_Nov04Ensembl.txt Loaded 298 elements of size 8 Sorted Creating table definition for wgEncodeNhgriBip Saving bed.tab Loading rn4 hgLoadBed rheMac2 wgEncodeNhgriBip Hg18_Rhesus_Jan06Ensembl.txt Reading Hg18_Rhesus_Jan06Ensembl.txt Loaded 385 elements of size 8 Sorted Creating table definition for wgEncodeNhgriBip Saving bed.tab Loading rheMac2 hgLoadBed canFam2 wgEncodeNhgriBip Hg18_Dog_May05Ensembl.txt Reading Hg18_Dog_May05Ensembl.txt Loaded 207 elements of size 8 Sorted Creating table definition for wgEncodeNhgriBip Saving bed.tab Loading canFam2 Could be simply wgEncodeNhgriBip in every DB (ie: panTro2.wgEncodeNhgriBip) Then simply need a table in each the tells what is available. Hg18_Chimp_Mar06Ensembl.txt Comparative Reference_Genome panTro2 Hg18_Cow_Oct07Ensembl.txt Comparative Reference_Genome bosTau4 Hg18_MM9_July07Ensembl.txt Comparative Reference_Genome mm9 Hg18_Rat_Nov04Ensembl.txt Comparative Reference_Genome rn4 Hg18_Rhesus_Jan06Ensembl.txt Comparative Reference_Genome rheMac2 Hg18_Dog_May05Ensembl.txt Comparative Reference_Genome canFam2 select hg18.wgEncodeNhgriBip.name,hg18.wgEncodeNhgriBip.chrom,hg18.wgEncodeNhgriBip.chromStart,hg18.wgEncodeNhgriBip.chromEnd from hg18.wgEncodeNhgriBip, panTro2.wgEncodeNhgriBip, rheMac2.wgEncodeNhgriBip, mm9.wgEncodeNhgriBip, rn4.wgEncodeNhgriBip, canFam2.wgEncodeNhgriBip, bosTau4.wgEncodeNhgriBip where hg18.wgEncodeNhgriBip.name = panTro2.wgEncodeNhgriBip.name and hg18.wgEncodeNhgriBip.name = rheMac2.wgEncodeNhgriBip.name and hg18.wgEncodeNhgriBip.name = mm9.wgEncodeNhgriBip.name and hg18.wgEncodeNhgriBip.name = rn4.wgEncodeNhgriBip.name and hg18.wgEncodeNhgriBip.name = canFam2.wgEncodeNhgriBip.name and hg18.wgEncodeNhgriBip.name = bosTau4.wgEncodeNhgriBip.name limit 2; +-----------------+-------+------------+----------+ | name | chrom | chromStart | chromEnd | +-----------------+-------+------------+----------+ | TMEM112B:NCAPH2 | chr22 | 49288245 | 49308779 | | PHF5A:ACO2 | chr22 | 40185666 | 40254939 | +-----------------+-------+------------+----------+ 2 rows in set (0.00 sec) Elnitski 2009-04-27 =================== Just loaded the hg18 BiPs again, so renamed the tables rename table wgEncodeNhgriBip to wgEncodeNhgriBipOld; rename table wgEncodeNhgriBiPPromotersReferencegenomeHg18 to wgEncodeNhgriBip; And the files in the downloads dir: cd wgEncodeNhgriBip mv wgEncodeNhgriBip.hg18.bed8.gz wgEncodeNhgriBip.hg18.bed8.gz.old mv ../wgEncodeNhgriBiP/wgEncodeNhgriBiPPromotersReferencegenomeHg18.bed8.gz wgEncodeNhgriBip.hg18.bed8.gz rm -rf wgEncodeNhgriBiP /cluster/data/encode/pipeline/bin/encodeStatus.pl 294 displayed /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -skipAutoCreation -allowReloads x ../298 Redo old NREs in order to remove non-text in names 2009-07-17 ============================================================= cd 100 cp ElnitskiEBK562gamma.bed ElnitskiEBK562gamma_corrected.bed cp ElnitskiSilencerK562gamma.bed ElnitskiSilencerK562gamma_corrected.bed edit to replace non-UTF8 characters rename table wgEncodeNhgriNRESilencersK562Ggamma to wgEncodeNhgriNRESilencersK562Ggamma_old; rename table wgEncodeNhgriNREEnhancerBlockersK562Ggamma to wgEncodeNhgriNREEnhancerBlockersK562Ggamma_old; /cluster/data/encode/pipeline/bin/doEncodeValidate.pl -quick -allowReloads x ../100 > validate_error 2>&1 & /cluster/data/encode/pipeline/bin/doEncodeLoad.pl x ../100 > load_error 2>&1 & rename table wgEncodeNhgriNRESilencersK562Ggamma_100 to wgEncodeNhgriNRESilencersK562Ggamma; rename table wgEncodeNhgriNREEnhancerBlockersK562Ggamma_100 to wgEncodeNhgriNREEnhancerBlockersK562Ggamma; # in downloads dir, files were loaded to wgEncodeNhgriNRE instead of the proper wgEncodeNhgriNre # moved old fils to "old" dir # moved new files to proper name and location rm -rf wgEncodeNhgriNRE # Oops, ElnitskiSilencerK562gamma_corrected.bed was not correctedf (a '-' was not actually a '-'!)... drop table wgEncodeNhgriNRESilencersK562Ggamma; rename table wgEncodeNhgriNRESilencersK562Ggamma_100 to wgEncodeNhgriNRESilencersK562Ggamma; drop table wgEncodeNhgriNREEnhancerBlockersK562Ggamma_100; /cluster/data/encode/pipeline/bin/encodeStatus.pl 100 approved /cluster/data/encode/pipeline/bin/encodeStatus.pl 100 reviewing Released: ========= /cluster/data/encode/pipeline/bin/encodeStatus.pl 200 released /cluster/data/encode/pipeline/bin/encodeStatus.pl 294 released 2009-10-02 Finally get around to marking NREs as released ========================================================= /cluster/data/encode/pipeline/bin/encodeStatus.pl 100 released