Commit 79544692 authored by Lena Hersemann's avatar Lena Hersemann

project -> PRJ_NAME

parent 57a0d8c0
......@@ -191,12 +191,12 @@ plotCorrelation --corData bin_data.npz --plotFile bc.pdf --corMethod spearman --
#EOF
#echo "cmd is $bcCmd"
#mysub "${project}__bamcorrelate" "$bcCmd" -q long -n 4 -R span[hosts=1] | blockScript .bamcorrelate
#mysub "${PRJ_NAME}__bamcorrelate" "$bcCmd" -q long -n 4 -R span[hosts=1] | blockScript .bamcorrelate
## old lsf version
#jl submit --wait --jl .bamcorrelate -q long -t 4 -n "${project}__bamcorrelate" "$bcCmd"
#jl submit --wait --jl .bamcorrelate -q long -t 4 -n "${PRJ_NAME}__bamcorrelate" "$bcCmd"
jl reset .bamcorrelate
jl submit --jl .bamcorrelate --wait -w 10:00 -t 4 -n "${project}__bamcorrelate" "$bcCmd"
jl submit --jl .bamcorrelate --wait -w 10:00 -t 4 -n "${PRJ_NAME}__bamcorrelate" "$bcCmd"
}
export -f dge_bam_correlate
......@@ -233,7 +233,7 @@ for bamFile in $bamFiles; do
sample=$(basename $bamFile .bam)
echo "converting $bamFile to bigwig format"
jl submit -j .bigwig -w 10:00 -n "${project}__bw__${sample}" "genomeCoverageBed -split -bg -ibam $bamFile -g ${genomeFai} | wigToBigWig -clip stdin ${genomeFai} ${sample}.bw"
jl submit -j .bigwig -w 10:00 -n "${PRJ_NAME}__bw__${sample}" "genomeCoverageBed -split -bg -ibam $bamFile -g ${genomeFai} | wigToBigWig -clip stdin ${genomeFai} ${sample}.bw"
done
jl wait --report .bigwig
......@@ -263,7 +263,7 @@ for bamFile in $bamFiles; do
sample=$(basename $bamFile .bam)
echo "converting $bamFile to bigwig format"
jl submit -j .bigwig -w 10:00 -n "${project}__bw__${sample}" "bamCoverage --bam ${bamFile} --binSize 10 -p 1 -o ${sample}.bw"
jl submit -j .bigwig -w 10:00 -n "${PRJ_NAME}__bw__${sample}" "bamCoverage --bam ${bamFile} --binSize 10 -p 1 -o ${sample}.bw"
done
jl wait --report .bigwig
......@@ -341,13 +341,13 @@ dge_create_star_index(){
# chmod +w $(dirname ${star_index})
mailme "${project}: creating STAR index in ${star_index}"
mailme "${PRJ_NAME}: creating STAR index in ${star_index}"
mkdir ${star_index}
cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 5"
#eval $cmd
#STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/Chromosomes/*.fa --runThreadN 10
jl submit --wait -t 5 -w 10:00 -m 50g -n "${project}_star_index" "$cmd"
jl submit --wait -t 5 -w 10:00 -m 50g -n "${PRJ_NAME}_star_index" "$cmd"
## prevent further modification
# chmod -w $(dirname ${star_index})
......
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