Commit 57a0d8c0 authored by Lena Hersemann's avatar Lena Hersemann

more robust PATH preparation

parent e3b0de32
......@@ -13,25 +13,35 @@ else
fi
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
export PATH=${BIO_BIN_BASE}/samtools-1.5:$PATH
export PATH=${BIO_BIN_BASE}/STAR-2.5.2b/source:$PATH
export PATH=${BIO_BIN_BASE}/ucsc:$PATH # for wigToBigWig
append2path(){
if [ ! -d ${1} ]; then
echo "can not append non-existing path '$1' to PATH" >&2
exit
fi
export PATH=/home/$(whoami)/local_bin/R-3.4.0/bin:$PATH
export PATH=$1:$PATH
}
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}/samtools-1.3
append2path ${BIO_BIN_BASE}/STAR-2.5.2b/source
append2path ${BIO_BIN_BASE}/ucsc
export PATH=/home/$(whoami)/local_bin/R-3.4.0/bin:$PATH
## Fixme use BIO_BIN_BASE for deeptools
## pip3 install --user deeptools
#export PATH=${BIO_BIN_BASE}/deepTools-2.2.2/bin:$PATH
export PATH=/home/$(whoami)/.local/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:$PATH
#export PATH=/projects/bioinfo/tools/joblist_v0.7:$PATH
append2path ${BIO_BIN_BASE}/joblist_v0.7
## make sure that rend.R is present
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/rendr/rendr_utils.sh 2>&1 2>/dev/null)
......@@ -186,7 +196,7 @@ plotCorrelation --corData bin_data.npz --plotFile bc.pdf --corMethod spearman --
## old lsf version
#jl submit --wait --jl .bamcorrelate -q long -t 4 -n "${project}__bamcorrelate" "$bcCmd"
jl reset .bamcorrelate
jl submit --jl .bamcorrelate -w 10:00 -t 4 -n "${project}__bamcorrelate" "$bcCmd"
jl submit --jl .bamcorrelate --wait -w 10:00 -t 4 -n "${project}__bamcorrelate" "$bcCmd"
}
export -f dge_bam_correlate
......@@ -213,8 +223,6 @@ if [ ! -f "${genomeFai}" ]; then
echo "could not find fai index $1! ${usage}" >&2 ; return;
fi
## add bigwig to PATH
export PATH=~/bin:${PATH}
if [ -z "$(which wigToBigWig 2>/dev/null)" ]; then
echo "could not find wigToBigWig in PATH! ${usage}" >&2 ; #return;
......
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