Commit 474a5f59 authored by Adam Caprez's avatar Adam Caprez
Browse files

Add .'ing of Lmod init script

Condor jobs do not see normal user shell init scripts.  Have to
explicitly dot it in for module to work.
parent 5e4d0e41
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load bedtools
bedtools "$@"
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load bowtie
bowtie2 "$@"
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load bwa
bwa "$@"
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load python/2.7 macs2
macs2 "$@"
......@@ -2,6 +2,7 @@
set -eu -o pipefail
set -o pipefail
. /util/opt/lmod/lmod/init/profile
module load picard
java=java
......
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load R spp
Rscript ${SPP_NODUPS} "$@"
#!/bin/bash
. /util/opt/lmod/lmod/init/profile
module load samtools
samtools "$@"
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