#!/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
