Commit 0715cb6a authored by Lena Hersemann's avatar Lena Hersemann

added path to bowtie-1.1.2; corrected "runThreadN 5"

parent 3ba0c079
......@@ -13,7 +13,7 @@ else
export PATH=${BIO_BIN_BASE}/bowtie-1.1.2:$PATH
export PATH=${BIO_BIN_BASE}/bowtie2-2.2.5:$PATH
export PATH=${BIO_BIN_BASE}/FastQC_0.11.2:$PATH
export PATH=${BIO_BIN_BASE}/bedtools2-2.25.0/bin/:$PATH
......@@ -336,7 +336,7 @@ dge_create_star_index(){
mailme "${project}: creating STAR index in ${star_index}"
mkdir ${star_index}
cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 10"
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"
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