Commit 6d208308 authored by Holger Brandl's avatar Holger Brandl

removed jl backward compatibility wrappers

parent 7c63e7cd
......@@ -38,22 +38,6 @@ source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/R/r
source <(curl https://raw.githubusercontent.com/holgerbrandl/datautils/v1.39/bash/core_utils.sh 2>&1 2>/dev/null)
## backward compatibility wrappers for old shell cluster utils
#joblist(){
# jl add $*
#}
#export -f joblist
#
#
#wait4jobs(){
# jl wait $*
#}
#export -f wait4jobs
# which tophat; which bowtie2; which cuffdiff
mcdir(){
if [ ! -d "$1" ]; then
mkdir "$1";
......@@ -318,7 +302,8 @@ dge_create_star_index(){
echo "Usage: dge_create_star_index <igenome>" >&2 ; return;
fi
igenome=$1
#igenome="Pan_troglodytes/Ensembl_81/CHIMP2.1.4"
local igenome=$1
if [ ! -d "$igenome" ] | [ ! -d "${igenome}/Sequence" ]; then
echo "igenome directory '$igenome' does not exist" >&2 ; return;
......@@ -338,6 +323,7 @@ dge_create_star_index(){
cmd="STAR --runMode genomeGenerate --genomeDir ${star_index} --genomeFastaFiles ${igenome}/Sequence/WholeGenomeFasta/genome.fa --runThreadN 5"
#eval $cmd
#echo $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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