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leekgroup · Apr 2, 2016 · 09d7d7d · 09d7d7d
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Showing 15 changed files with 17 additions and 17 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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
@@ -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