From 09d7d7dcad76c5f675591ef54480c97afc65f4df Mon Sep 17 00:00:00 2001 From: lcolladotor Date: Sat, 2 Apr 2016 08:47:18 -0400 Subject: [PATCH] Switch to dcl01 disk --- hippo/counts-gene/run.sh | 4 ++-- optional1-sortSam.sh | 2 +- optional2-HTSeq.sh | 2 +- optional3-summOv.R | 2 +- optional3-summOv.sh | 2 +- step1-fullCoverage.sh | 2 +- step2-makeModels.sh | 2 +- step3-analyzeChr.sh | 2 +- step4-mergeResults.sh | 4 ++-- step5-derfinderReport.sh | 2 +- step6-regionMatrix.sh | 2 +- step7-regMatVsDERs.sh | 2 +- step8-coverageToExon.sh | 2 +- step9-summaryInfo.R | 2 +- step9-summaryInfo.sh | 2 +- 15 files changed, 17 insertions(+), 17 deletions(-) diff --git a/hippo/counts-gene/run.sh b/hippo/counts-gene/run.sh index 1fd3b24..8484a69 100755 --- a/hippo/counts-gene/run.sh +++ b/hippo/counts-gene/run.sh @@ -8,14 +8,14 @@ echo "**** Job starts ****" date -mkdir -p /dcs01/ajaffe/Brain/derRuns/derSoftware/hippo/counts-gene/logs +mkdir -p /dcl01/lieber/ajaffe/derRuns/derSoftware/hippo/counts-gene/logs ## Summarize overlaps module load R/3.2.x Rscript counts-gene.R # Move log files into the logs directory -mv /dcs01/ajaffe/Brain/derRuns/derSoftware/hippo/counts-gene/summOv-hippo-rerun.* /dcs01/ajaffe/Brain/derRuns/derSoftware/hippo/counts-gene/logs/ +mv /dcl01/lieber/ajaffe/derRuns/derSoftware/hippo/counts-gene/summOv-hippo-rerun.* /dcl01/lieber/ajaffe/derRuns/derSoftware/hippo/counts-gene/logs/ ### Done echo "**** Job ends ****" diff --git a/optional1-sortSam.sh b/optional1-sortSam.sh index b0d4626..315fa3b 100755 --- a/optional1-sortSam.sh +++ b/optional1-sortSam.sh @@ -9,7 +9,7 @@ EXPERIMENT=$1 SHORT="sortSam-${EXPERIMENT}" # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/sortSam diff --git a/optional2-HTSeq.sh b/optional2-HTSeq.sh index 996f1cb..ef8eb55 100755 --- a/optional2-HTSeq.sh +++ b/optional2-HTSeq.sh @@ -9,7 +9,7 @@ EXPERIMENT=$1 SHORT="HTSeq-${EXPERIMENT}" # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/HTSeq diff --git a/optional3-summOv.R b/optional3-summOv.R index 7c697e1..11a656b 100644 --- a/optional3-summOv.R +++ b/optional3-summOv.R @@ -6,7 +6,7 @@ library("derfinder") library("GenomicRanges") ## Load pre-computed exonic parts from Ensembl annotation -# load("/dcs01/ajaffe/Brain/derRuns/derMisc/ensemblExons/exonicParts.Rdata") +# load("/dcl01/lieber/ajaffe/derRuns/derMisc/ensemblExons/exonicParts.Rdata") ## For comparability, use the exons from genomic state load("/home/epi/ajaffe/Lieber/Projects/RNAseq/derannotator/rdas/GenomicState.Hsapiens.ensembl.GRCh37.p11.rda") diff --git a/optional3-summOv.sh b/optional3-summOv.sh index 214af8d..f5dda51 100755 --- a/optional3-summOv.sh +++ b/optional3-summOv.sh @@ -9,7 +9,7 @@ EXPERIMENT=$1 SHORT="summOv-${EXPERIMENT}" # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/summOv diff --git a/step1-fullCoverage.sh b/step1-fullCoverage.sh index 06f62d9..db18cc2 100755 --- a/step1-fullCoverage.sh +++ b/step1-fullCoverage.sh @@ -11,7 +11,7 @@ SHORT="fullCov-${EXPERIMENT}" CORES=10 # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/CoverageInfo diff --git a/step2-makeModels.sh b/step2-makeModels.sh index 951594c..91142bd 100755 --- a/step2-makeModels.sh +++ b/step2-makeModels.sh @@ -10,7 +10,7 @@ SHORT="derMod-${EXPERIMENT}" PREFIX=$2 # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/derAnalysis diff --git a/step3-analyzeChr.sh b/step3-analyzeChr.sh index 501a5d2..4b8c182 100755 --- a/step3-analyzeChr.sh +++ b/step3-analyzeChr.sh @@ -10,7 +10,7 @@ SHORT="derA-${EXPERIMENT}" PREFIX=$2 # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/derAnalysis DATADIR=${MAINDIR}/CoverageInfo diff --git a/step4-mergeResults.sh b/step4-mergeResults.sh index 07e22fb..bcc9084 100755 --- a/step4-mergeResults.sh +++ b/step4-mergeResults.sh @@ -10,7 +10,7 @@ SHORT="derM-${EXPERIMENT}" PREFIX=$2 # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/derAnalysis @@ -34,7 +34,7 @@ mkdir -p ${WDIR}/${outdir}/logs # merge results cd ${WDIR} module load R/3.2.x -Rscript -e "library(derfinder); load('/dcs01/ajaffe/Brain/derRuns/derfinderExample/derGenomicState/GenomicState.Hsapiens.UCSC.hg19.knownGene.Rdata'); load('${WDIR}/${PREFIX}/chr22/optionsStats.Rdata'); chrs <- c(1:22, 'X', 'Y'); mergeResults(chrs = chrs, prefix = '${PREFIX}', genomicState = GenomicState.Hsapiens.UCSC.hg19.knownGene[['fullGenome']], optionsStats = optionsStats); Sys.time(); proc.time(); options(width = 120); devtools::session_info()" +Rscript -e "library(derfinder); load('/dcl01/lieber/ajaffe/derRuns/derfinderExample/derGenomicState/GenomicState.Hsapiens.UCSC.hg19.knownGene.Rdata'); load('${WDIR}/${PREFIX}/chr22/optionsStats.Rdata'); chrs <- c(1:22, 'X', 'Y'); mergeResults(chrs = chrs, prefix = '${PREFIX}', genomicState = GenomicState.Hsapiens.UCSC.hg19.knownGene[['fullGenome']], optionsStats = optionsStats); Sys.time(); proc.time(); options(width = 120); devtools::session_info()" # Move log files into the logs directory mv ${ROOTDIR}/${sname}.* ${WDIR}/${outdir}/logs/ diff --git a/step5-derfinderReport.sh b/step5-derfinderReport.sh index a83cb83..98d77da 100755 --- a/step5-derfinderReport.sh +++ b/step5-derfinderReport.sh @@ -10,7 +10,7 @@ SHORT="derR-${EXPERIMENT}" PREFIX=$2 # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/derAnalysis diff --git a/step6-regionMatrix.sh b/step6-regionMatrix.sh index 8078f9c..6298561 100755 --- a/step6-regionMatrix.sh +++ b/step6-regionMatrix.sh @@ -11,7 +11,7 @@ ncore=5 cores="${ncore}cores" # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/regionMatrix diff --git a/step7-regMatVsDERs.sh b/step7-regMatVsDERs.sh index 88d0182..cfbf96c 100755 --- a/step7-regMatVsDERs.sh +++ b/step7-regMatVsDERs.sh @@ -10,7 +10,7 @@ ncore=5 cores="${ncore}cores" # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} # Construct shell files diff --git a/step8-coverageToExon.sh b/step8-coverageToExon.sh index 2c4d12e..adfd4d6 100755 --- a/step8-coverageToExon.sh +++ b/step8-coverageToExon.sh @@ -10,7 +10,7 @@ SHORT="covToEx-${EXPERIMENT}" CORES=1 # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} WDIR=${MAINDIR}/coverageToExon diff --git a/step9-summaryInfo.R b/step9-summaryInfo.R index dbfc0bd..2049b25 100644 --- a/step9-summaryInfo.R +++ b/step9-summaryInfo.R @@ -79,7 +79,7 @@ if (is.null(opt$verbose)) opt$verbose <- TRUE startTime <- Sys.time() ## Paths -rootdir <- '/dcs01/ajaffe/Brain/derRuns/derCountSupp' +rootdir <- '/dcl01/lieber/ajaffe/derRuns/derCountSupp' resdir <- file.path(rootdir, opt$short, 'summaryInfo', opt$run) ## results path diff --git a/step9-summaryInfo.sh b/step9-summaryInfo.sh index da0ed76..a638c7c 100644 --- a/step9-summaryInfo.sh +++ b/step9-summaryInfo.sh @@ -8,7 +8,7 @@ PREFIX=$2 SHORT="summInfo-${EXPERIMENT}" # Directories -ROOTDIR=/dcs01/ajaffe/Brain/derRuns/derCountSupp +ROOTDIR=/dcl01/lieber/ajaffe/derRuns/derCountSupp MAINDIR=${ROOTDIR}/${EXPERIMENT} # Construct shell files