Commit ea53f611 authored by Lena Hersemann's avatar Lena Hersemann

added bedtools2-2.25 and reset of joblist task name before running dge_bigwig

parent 79544692
......@@ -25,7 +25,7 @@ append2path(){
append2path ${BIO_BIN_BASE}/bowtie-1.1.2
append2path ${BIO_BIN_BASE}/bowtie2-2.2.5
append2path ${BIO_BIN_BASE}/FastQC_0.11.2
append2path ${BIO_BIN_BASE}/bedtools2-2.25.0/bin/
append2path ${BIO_BIN_BASE}/bedtools2-2.25.0/bin
append2path ${BIO_BIN_BASE}/samtools-1.3
append2path ${BIO_BIN_BASE}/STAR-2.5.2b/source
append2path ${BIO_BIN_BASE}/ucsc
......@@ -38,7 +38,6 @@ export PATH=/home/$(whoami)/local_bin/R-3.4.0/bin:$PATH
export PATH=/home/$(whoami)/.local/bin:$PATH
#export PATH=/home/brandl/bin/subread-1.4.6-p3-Linux-x86_64/bin:$PATH
## add cluster job manager
#export PATH=/projects/bioinfo/tools/joblist_v0.7:$PATH
append2path ${BIO_BIN_BASE}/joblist_v0.7
......@@ -228,6 +227,8 @@ if [ -z "$(which wigToBigWig 2>/dev/null)" ]; then
echo "could not find wigToBigWig in PATH! ${usage}" >&2 ; #return;
fi
jl reset .bigwig
## create big wig files
for bamFile in $bamFiles; do
sample=$(basename $bamFile .bam)
......
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