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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,5 @@ | ||
| #!/bin/bash | ||
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| LDSTORE="${HOME}/packages/ldstore/ldstore_v1.1_x86_64/ldstore" | ||
| TEJAAS="${HOME}/trans-eQTL/codebase/tejaas/bin/tejaas" | ||
| GNETLMMDIR="${HOME}/packages/GNetLMM" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,18 +1,17 @@ | ||
| #!/bin/bash | ||
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| CURDIR=`pwd` | ||
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| # external programs required for the pipeline | ||
| LDSTORE="${HOME}/packages/ldstore/ldstore_v1.1_x86_64/ldstore" | ||
| TEJAAS="${HOME}/trans-eQTL/codebase/tejaas/bin/tejaas" | ||
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| # Pipeline directories | ||
| UTILSDIR="${CURDIR}/utils" | ||
| CONFIGDIR="${CURDIR}/configs" | ||
| SCRIPTDIR="${CURDIR}/../scripts" | ||
| MASTER_BSUBDIR="${CURDIR}/../bsubfiles" | ||
| JOBSUBDIR="${CURDIR}/../jobsubs" | ||
| ANALYSISDIR="${CURDIR}/../analysis" | ||
| CURDIRUP="$(dirname "$(pwd)")" | ||
| UTILSDIR="${CURDIRUP}/main/utils" | ||
| CONFIGDIR="${CURDIRUP}/main/configs" | ||
| SCRIPTDIR="${CURDIRUP}/scripts" | ||
| MASTER_BSUBDIR="${CURDIRUP}/bsubfiles" | ||
| JOBSUBDIR="${CURDIRUP}/jobsubs" | ||
| ANALYSISDIR="${CURDIRUP}/analysis" | ||
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| # Script files | ||
| MATRIXEQTL="${SCRIPTDIR}/matrixeqtl.R" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,81 @@ | ||
| #!/bin/bash | ||
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| function submit_tejaas() { | ||
| local tejaas=$1 | ||
| local chrm=$2 | ||
| local genotype=$3 | ||
| local expression=$4 | ||
| local sample=$5 | ||
| local geneinfo=$6 | ||
| local maffile=$7 | ||
| local method=$8 | ||
| local null=$9 | ||
| local snpthres=${10} | ||
| local genethres=${11} | ||
| local sbeta=${12} | ||
| local extraflags=${13} | ||
| local jobsubdir=${14} | ||
| local outdir=${15} | ||
| local jobprefix=${16} | ||
| local nmax=${17} | ||
| local thisjobdep=${18} | ||
| local bsubdir=${19} | ||
| local __jobdeps=${20} | ||
| local jobdeps=${21} | ||
| local jobname=0 | ||
| local i=0 | ||
| local index=0 | ||
| local includesnps=0 | ||
| local startsnp=0 | ||
| local endsnp=0 | ||
| local outprefix=0 | ||
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| ## echo $tejaas $chrm $genotype ${expression} ${sample} ${geneinfo} $maffile | ||
| ## echo "Method: " ${method} ${null} ${snpthres} ${genethres} ${sbeta} | ||
| ## echo "Extraflags: " ${extraflags} | ||
| ## echo $jobsubdir $outdir $jobprefix | ||
| ## echo $nmax $thisjobdep $bsubdir $__jobdeps $jobdeps | ||
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| ntot=`zcat ${genotype} | wc -l` | ||
| njobs=$(echo $(( ntot/nmax ))) | ||
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| if [ -d ${jobsubdir} ]; then rm -rf ${jobsubdir}; fi; mkdir -p ${jobsubdir} | ||
| if [ ! -d ${outdir} ]; then mkdir -p ${outdir}; fi | ||
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| for (( i=0; i <= ${njobs}; i++ )); do | ||
| index=`echo ${i} | awk '{printf "%03d", $1}'` | ||
| jobname="${jobprefix}_${index}" | ||
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| startsnp=$(( nmax * i + 1 )) | ||
| endsnp=$(( nmax * (i + 1) )) | ||
| if [ $endsnp -gt $ntot ]; then | ||
| endsnp=${ntot} | ||
| fi | ||
| includesnps="${startsnp}:${endsnp}" | ||
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| outprefix="${outdir}/chunk${index}" | ||
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| # create the job submission file | ||
| sed "s|_i_NAME|${jobname}|g; | ||
| s|_TJS_BINR|${tejaas}|g; | ||
| s|_GT_FILE_|${genotype}|g; | ||
| s|_SAM_FILE|${sample}|g; | ||
| s|_EXPR_FL_|${expression}|g; | ||
| s|_GEN_POSF|${geneinfo}|g; | ||
| s|_TJ_METHD|${method}|g; | ||
| s|_NULL_MDL|${null}|g; | ||
| s|_OUT_PRFX|${outprefix}|g; | ||
| s|_STRT_END|${includesnps}|g; | ||
| s|_SNP_CUT_|${snpthres}|g; | ||
| s|_GEN_CUT_|${genethres}|g; | ||
| s|_SIG_BETA|${sbeta}|g; | ||
| s|_CHRM_NUM|${chrm}|g; | ||
| s|_MAF_FILE|${maffile}|g; | ||
| s|_EXT_FLAG|\"${extraflags}\"|g; | ||
| " ${bsubdir}/tejaas.bsub > ${jobsubdir}/${jobname}.bsub | ||
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| submit_job ${jobsubdir} ${jobname} ${thisjobdep} | ||
| jobdeps=`add_deps "${jobdeps}" ${jobname}` | ||
| done | ||
| eval $__jobdeps="'$jobdeps'" | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,66 +1,65 @@ | ||
| #!/bin/bash | ||
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| THISMETHOD="tejaas" | ||
| THISJOBDEPS="" | ||
| THISJOBDEPS="None" | ||
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| source ${UTILSDIR}/submit_tejaas | ||
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| for CHRM in ${CHRNUMS}; do | ||
| GENOTYPEFILE=${GENO_FMT/\[CHRM\]/${CHRM}} | ||
| TOTALSNPS=`zcat ${GENOTYPEFILE} | wc -l` | ||
| NJOBS=$(echo $(( TOTALSNPS/MAX_NSNP_PERJOB ))) | ||
| MAF_1KG_FILE=${MAF_1KG_FMT/\[CHRM\]/${CHRM}} | ||
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| for NULL in ${TEJAAS_NULL}; do | ||
| for SBETA in ${TEJAAS_SIGMA_BETA}; do | ||
| if [ "${RUNJPA}" = "true" ]; then | ||
| METHOD_VARIANT="jpa" | ||
| SPECIFIC_JOBSUBDIR="${JOBSUBDIR_DATA}/${THISMETHOD}/${METHOD_VARIANT}/chr${CHRM}" | ||
| SPECIFIC_OUTDIR="${OUTDIR_DATA}/${THISMETHOD}/${METHOD_VARIANT}/chr${CHRM}" | ||
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| METHOD_VARIANT="${NULL}null_sb${SBETA}" | ||
| SPECIFIC_JOBSUBDIR="${JOBSUBDIR_DATA}/${THISMETHOD}/${METHOD_VARIANT}/chr${CHRM}" | ||
| SPECIFIC_OUTDIR="${OUTDIR_DATA}/${THISMETHOD}/${METHOD_VARIANT}/chr${CHRM}" | ||
| EXTRAFLAGS="--dosage" | ||
| if [ "${DATATYPE}" = "cardiogenics" ]; then | ||
| EXTRAFLAGS="$EXTRAFLAGS --trim" | ||
| fi | ||
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| if [ -d ${SPECIFIC_JOBSUBDIR} ]; then rm -rf ${SPECIFIC_JOBSUBDIR}; fi; mkdir -p ${SPECIFIC_JOBSUBDIR} | ||
| if [ ! -d ${SPECIFIC_OUTDIR} ]; then mkdir -p ${SPECIFIC_OUTDIR}; fi | ||
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| JOBPREFIX="${THISMETHOD}_${METHOD_VARIANT}_${MDATA}_chr${CHRM}_${RANDSTRING}" | ||
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| for (( JOB=0; JOB <= ${NJOBS}; JOB++ )); do | ||
| INDEX=`echo ${JOB} | awk '{printf "%03d", $1}'` | ||
| JOBNAME="${JOBPREFIX}_${INDEX}" | ||
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| STARTSNP=$(( MAX_NSNP_PERJOB * JOB + 1 )) | ||
| ENDSNP=$(( MAX_NSNP_PERJOB * (JOB+1) )) | ||
| if [ $ENDSNP -gt $TOTALSNPS ]; then | ||
| ENDSNP=${TOTALSNPS} | ||
| fi | ||
| INCSNP="${STARTSNP}:${ENDSNP}" | ||
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| OUTPREFIX="${SPECIFIC_OUTDIR}/chunk${INDEX}" | ||
| JOBPREFIX="${THISMETHOD}_${METHOD_VARIANT}_${MDATA}_chr${CHRM}_${RANDSTRING}" | ||
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| submit_tejaas ${TEJAAS} ${CHRM} ${GENOTYPEFILE} ${EXPRESSIONFILE} ${SAMPLEFILE} \ | ||
| ${GENEINFOFILE} ${MAF_1KG_FILE} \ | ||
| jpa perm \ | ||
| ${TEJAAS_SNPS_THRES} ${TEJAAS_GENE_THRES} 0.01 \ | ||
| "${EXTRAFLAGS}" \ | ||
| ${SPECIFIC_JOBSUBDIR} ${SPECIFIC_OUTDIR} ${JOBPREFIX} \ | ||
| ${MAX_NSNP_PERJOB} \ | ||
| ${THISJOBDEPS} ${MASTER_BSUBDIR} \ | ||
| JOBDEPS "${JOBDEPS}" | ||
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| else | ||
| for NULL in ${TEJAAS_NULL}; do | ||
| for SBETA in ${TEJAAS_SIGMA_BETA}; do | ||
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| METHOD_VARIANT="${NULL}null_sb${SBETA}" | ||
| SPECIFIC_JOBSUBDIR="${JOBSUBDIR_DATA}/${THISMETHOD}/${METHOD_VARIANT}/chr${CHRM}" | ||
| SPECIFIC_OUTDIR="${OUTDIR_DATA}/${THISMETHOD}/${METHOD_VARIANT}/chr${CHRM}" | ||
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| EXTRAFLAGS="--dosage" | ||
| if [ "${DATATYPE}" = "cardiogenics" ]; then | ||
| EXTRAFLAGS="$EXTRAFLAGS --trim" | ||
| fi | ||
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| # create the job submission file | ||
| sed "s|_JOB_NAME|${JOBNAME}|g; | ||
| s|_TJS_BINR|${TEJAAS}|g; | ||
| s|_GT_FILE_|${GENOTYPEFILE}|g; | ||
| s|_SAM_FILE|${SAMPLEFILE}|g; | ||
| s|_EXPR_FL_|${EXPRESSIONFILE}|g; | ||
| s|_GEN_POSF|${GENEINFOFILE}|g; | ||
| s|_TJ_METHD|${TEJAAS_MODEL}|g; | ||
| s|_NULL_MDL|${NULL}|g; | ||
| s|_OUT_PRFX|${OUTPREFIX}|g; | ||
| s|_STRT_END|${INCSNP}|g; | ||
| s|_SNP_CUT_|${TEJAAS_SNPS_THRES}|g; | ||
| s|_GEN_CUT_|${TEJAAS_GENE_THRES}|g; | ||
| s|_SIG_BETA|${SBETA}|g; | ||
| s|_CHRM_NUM|${CHRM}|g; | ||
| s|_MAF_FILE|${MAF_1KG_FILE}|g; | ||
| s|_EXT_FLAG|\"${EXTRAFLAGS}\"|g; | ||
| " ${MASTER_BSUBDIR}/tejaas.bsub > ${SPECIFIC_JOBSUBDIR}/${JOBNAME}.bsub | ||
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| submit_job ${SPECIFIC_JOBSUBDIR} ${JOBNAME} ${THISJOBDEPS} | ||
| JOBDEPS=`add_deps "${JOBDEPS}" ${JOBNAME}` | ||
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| JOBPREFIX="${THISMETHOD}_${METHOD_VARIANT}_${MDATA}_chr${CHRM}_${RANDSTRING}" | ||
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| submit_tejaas ${TEJAAS} ${CHRM} ${GENOTYPEFILE} ${EXPRESSIONFILE} ${SAMPLEFILE} \ | ||
| ${GENEINFOFILE} ${MAF_1KG_FILE} \ | ||
| ${TEJAAS_MODEL} ${NULL} \ | ||
| ${TEJAAS_SNPS_THRES} ${TEJAAS_GENE_THRES} ${SBETA}\ | ||
| "${EXTRAFLAGS}" \ | ||
| ${SPECIFIC_JOBSUBDIR} ${SPECIFIC_OUTDIR} ${JOBPREFIX} \ | ||
| ${MAX_NSNP_PERJOB} \ | ||
| ${THISJOBDEPS} ${MASTER_BSUBDIR} \ | ||
| JOBDEPS "${JOBDEPS}" | ||
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| done | ||
| done | ||
| done | ||
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| fi | ||
| done | ||
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| RUNJPA=false |