ce163cf46702cd8fea306a972ce85ceaff19e41d kent Mon Sep 30 19:09:53 2024 -0700 Updating CDW main README and adding install instructions and a script. diff --git src/hg/cirm/cdw/install/initQa src/hg/cirm/cdw/install/initQa new file mode 100755 index 0000000..71860c2 --- /dev/null +++ src/hg/cirm/cdw/install/initQa @@ -0,0 +1,93 @@ +#!/bin/tcsh -efx +cdwAddAssembly 9606 hg38 hg38 /data/cirm/valData/hg38/hg38.2bit -givenMd5=8c0d7fe26540718c381a8d458274f270 +cdwAddAssembly 10090 mm9 mm9 /data/cirm/valData/mm9/mm9.2bit -givenMd5=e47354d24b9d95e832c337d42b9f8f71 +cdwAddAssembly 10090 mm10 mm10 /data/cirm/valData/mm10/mm10.2bit -givenMd5=fcfcc276799031793a513e2e9c07adad +cdwAddAssembly 10116 rn4 rn4 /data/cirm/valData/rn4/rn4.2bit -givenMd5=9f0ed3cd87ab900be5e8157dbeaee12e +cdwAddAssembly 7227 dm6 dm6 /data/cirm/valData/dm6/dm6.2bit -givenMd5=a2855251bb81479b1742dbbbd575fdcc +cdwAddAssembly 559292 sacCer3 sacCer3 /data/cirm/valData/sacCer3/sacCer3.2bit -givenMd5=880201a7d1ec95c0185b0b4783c80411 +cdwAddAssembly 6239 ce10 ce10 /data/cirm/valData/ce10/ce10.2bit -givenMd5=3d0bab4bc255fc5b3276a476e13d230c +cdwAddAssembly 562 escCol1 escCol1 /data/cirm/valData/escCol1/escCol1.2bit +exit +cdwAddQaEnrichTarget open hg19 /data/cirm/valData/hg19/regions/open.bb +cdwAddQaEnrichTarget exon hg19 /data/cirm/valData/hg19/regions/exon.bb +cdwAddQaEnrichTarget promoter hg19 /data/cirm/valData/hg19/regions/promoter.bb +cdwAddQaEnrichTarget coding hg19 /data/cirm/valData/hg19/regions/coding.bb +cdwAddQaEnrichTarget intron hg19 /data/cirm/valData/hg19/regions/intron.bb +cdwAddQaEnrichTarget utr hg19 /data/cirm/valData/hg19/regions/utr.bb +cdwAddQaEnrichTarget utr3 hg19 /data/cirm/valData/hg19/regions/utr3.bb +cdwAddQaEnrichTarget utr5 hg19 /data/cirm/valData/hg19/regions/utr5.bb +cdwAddQaEnrichTarget chrM hg19 /data/cirm/valData/hg19/regions/chrM.bb +cdwAddQaEnrichTarget chrX hg19 /data/cirm/valData/hg19/regions/chrX.bb +cdwAddQaEnrichTarget chrY hg19 /data/cirm/valData/hg19/regions/chrY.bb +cdwAddQaEnrichTarget common_snp hg19 /data/cirm/valData/hg19/regions/common_snp.bb +cdwAddQaEnrichTarget open mm9 /data/cirm/valData/mm9/regions/open.bb +cdwAddQaEnrichTarget exon mm9 /data/cirm/valData/mm9/regions/exon.bb +cdwAddQaEnrichTarget promoter mm9 /data/cirm/valData/mm9/regions/promoter.bb +cdwAddQaEnrichTarget coding mm9 /data/cirm/valData/mm9/regions/coding.bb +cdwAddQaEnrichTarget intron mm9 /data/cirm/valData/mm9/regions/intron.bb +cdwAddQaEnrichTarget utr3 mm9 /data/cirm/valData/mm9/regions/utr3.bb +cdwAddQaEnrichTarget utr5 mm9 /data/cirm/valData/mm9/regions/utr5.bb +cdwAddQaEnrichTarget utr mm9 /data/cirm/valData/mm9/regions/utr.bb +cdwAddQaEnrichTarget chrM mm9 /data/cirm/valData/mm9/regions/chrM.bb +cdwAddQaEnrichTarget chrX mm9 /data/cirm/valData/mm9/regions/chrX.bb +cdwAddQaEnrichTarget chrY mm9 /data/cirm/valData/mm9/regions/chrY.bb +cdwAddQaEnrichTarget common_snp mm9 /data/cirm/valData/mm9/regions/common_snp.bb +cdwAddQaEnrichTarget open mm10 /data/cirm/valData/mm10/regions/open.bb +cdwAddQaEnrichTarget exon mm10 /data/cirm/valData/mm10/regions/exon.bb +cdwAddQaEnrichTarget promoter mm10 /data/cirm/valData/mm10/regions/promoter.bb +cdwAddQaEnrichTarget coding mm10 /data/cirm/valData/mm10/regions/coding.bb +cdwAddQaEnrichTarget intron mm10 /data/cirm/valData/mm10/regions/intron.bb +cdwAddQaEnrichTarget utr3 mm10 /data/cirm/valData/mm10/regions/utr3.bb +cdwAddQaEnrichTarget utr5 mm10 /data/cirm/valData/mm10/regions/utr5.bb +cdwAddQaEnrichTarget utr mm10 /data/cirm/valData/mm10/regions/utr.bb +cdwAddQaEnrichTarget chrM mm10 /data/cirm/valData/mm10/regions/chrM.bb +cdwAddQaEnrichTarget chrX mm10 /data/cirm/valData/mm10/regions/chrX.bb +cdwAddQaEnrichTarget chrY mm10 /data/cirm/valData/mm10/regions/chrY.bb +cdwAddQaEnrichTarget common_snp mm10 /data/cirm/valData/mm10/regions/common_snp.bb +cdwAddQaEnrichTarget open hg38 /data/cirm/valData/hg38/regions/open.bb +cdwAddQaEnrichTarget exon hg38 /data/cirm/valData/hg38/regions/exon.bb +cdwAddQaEnrichTarget promoter hg38 /data/cirm/valData/hg38/regions/promoter.bb +cdwAddQaEnrichTarget coding hg38 /data/cirm/valData/hg38/regions/coding.bb +cdwAddQaEnrichTarget intron hg38 /data/cirm/valData/hg38/regions/intron.bb +cdwAddQaEnrichTarget utr hg38 /data/cirm/valData/hg38/regions/utr.bb +cdwAddQaEnrichTarget utr3 hg38 /data/cirm/valData/hg38/regions/utr3.bb +cdwAddQaEnrichTarget utr5 hg38 /data/cirm/valData/hg38/regions/utr5.bb +cdwAddQaEnrichTarget chrM hg38 /data/cirm/valData/hg38/regions/chrM.bb +cdwAddQaEnrichTarget chrX hg38 /data/cirm/valData/hg38/regions/chrX.bb +cdwAddQaEnrichTarget chrY hg38 /data/cirm/valData/hg38/regions/chrY.bb +cdwAddQaEnrichTarget common_snp hg38 /data/cirm/valData/hg38/regions/common_snp.bb +cdwAddQaContamTarget hg19 +cdwAddQaContamTarget mm10 +cdwAddQaContamTarget escCol1 +cdwAddQaContamTarget dm6 +cdwAddQaContamTarget ce10 +cdwAddQaContamTarget rn4 +cdwAddQaContamTarget sacCer3 +hgsql cdw -e 'insert cdwLab (name,pi,institution,url) values ("quake", "Stephen Quake", "Stanford University", "http://thebigone.stanford.edu")' +#hgsql cdw -e 'insert cdwLab (name,pi,institution,url) values ("snyder", "Michael Snyder", "Stanford University", "http://snyderlab.stanford.edu")' +#hgsql cdw -e 'insert cdwLab (name,pi,institution,url) values ("stam", "John Stamatoyannopoulus", "University of Washington", "http://stamlab.org")' +hgsql cdw -e 'insert cdwLab (name,pi,institution,url) values ("kent", "W. James Kent", "UC Santa Cruz", "http://users.soe.ucsc.edu/~kent")' +hgsql cdw -e 'create view enrichedFiles as select f.id,v.format,v.enrichedIn,e.enrichment,left(f.submitFileName,70) submitFileName from cdwQaEnrich e,cdwValidFile v,cdwFile f,cdwQaEnrichTarget t where e.fileId=f.id and v.fileId=f.id and t.id=e.qaEnrichTargetId and v.enrichedIn=t.name;' +hgsql cdw -e 'create view crossEnrichments as select e.id aId,e.cdwFileName aFileName,y.id bId,y.cdwFileName bFileName,ev.enrichedIn enrich,sampleSampleEnrichment xEnrichment from cdwFile e,cdwQaPairSampleOverlap p, cdwFile y,cdwValidFile ev where e.id=p.elderFileId and y.id=p.youngerFileId and ev.fileId = e.id' +hgsql cdw -e 'create view correlations as select e.id aId,e.cdwFileName aFileName,y.id bId,y.cdwFileName bFileName,pearsonInEnriched from cdwFile e,cdwQaPairCorrelation p, cdwFile y where e.id=p.elderFileId and y.id=p.youngerFileId' +hgsql cdw -e 'create view vf as select e.id fileId,submitId,submitFileName,cdwFileName,FROM_UNIXTIME(endUploadTime) endUploadTime,FROM_UNIXTIME(updateTime) updateTime,size,md5,tags,errorMessage,deprecated,replacedBy,v.id validId,licensePlate,format,outputType,experiment,replicate,enrichedIn,ucscDb,itemCount,basesInItems,mapRatio,depth,singleQaStatus,replicateQaStatus,part,pairedEnd,qaVersion,uniqueMapRatio from cdwFile e, cdwValidFile v where e.id = v.fileId' + +hgsql cdw -e 'create view xf as select fileId,submitId,submitFileName,cdwFileName,endUploadTime endUploadTime,updateTime updateTime,size,md5,tags,errorMessage,deprecated,replacedBy,validId,licensePlate,format,outputType,experiment,replicate,enrichedIn,ucscDb,itemCount,basesInItems,mapRatio,depth,singleQaStatus,replicateQaStatus,part,pairedEnd,qaVersion,uniqueMapRatio,rfa,assayType,dataType,lab,biosample,ipTarget from vf,cdwExperiment ex where vf.experiment = ex.accession' + +#Add experiment table, just a local one rather than from stanford +#hgsql cdw -e 'load data local infile "../oneShot/rsyncCdwExpDataType/jan17.tab" into table cdwExperiment' +#hgsql cdw -e 'load data local infile "../oneShot/cdwFakeBiosample/jan3.tab" into table cdwBiosample' + + +## Add eap tables and run eap setup script +#hgsql cdw < ../../eap/lib/eapDb.sql +#../../eap/lib/addSoftware + +# TODO !!! There are 4 tables starting with cdwStep that are not created by the script. +# TODO Check out cdwStep.sql in this directory + +# Relaunch cdwRunDaemons. Send them initial wake up message +if (-e cdwQaAgent.log ) then + rm cdwQaAgent.log +endif +restartDaemons