Commit c26ca54f authored by Adam Caprez's avatar Adam Caprez
Browse files

Add cd'ing to correct directory

The BLAHP submit wrapper creates a temp directory and cd's there
before running the executable. This breaks Pegasus jobs for a
sharedfs site as it expects to be in the shared-scratch dir
via the `remote_iwd` Condor ClassAd.  This dir is available via
the PEGASUS_SCRATCH_DIR env variable in the job, so cd there as a
workaround.
parent 65ff36dd
#!/usr/bin/python
#!/bin/env python
import chipathlon.utils
import argparse
......
#!/bin/bash
cd $PEGASUS_SCRATCH_DIR
/bin/sort -k 8gr,8gr "$1" | awk 'BEGIN{OFS="\t"}{$r="PEAK_"NR; print $0;}' > "$2"
#!/bin/bash
cd $PEGASUS_SCRATCH_DIR
/bin/zcat "$1" | awk 'BEGIN{OFS="\t"}{print $1,int($2),int($3),$4,$5,$6,$7,$8,$9,$10;}' > "$2"
#!/bin/bash
cd $PEGASUS_SCRATCH_DIR
. /util/opt/lmod/lmod/init/profile
module load bedtools
bedtools "$@"
#!/bin/bash
cd $PEGASUS_SCRATCH_DIR
. /util/opt/lmod/lmod/init/profile
module load bowtie
bowtie2 "$@"
#!/bin/bash
cd $PEGASUS_SCRATCH_DIR
. /util/opt/lmod/lmod/init/profile
module load bwa
bwa "$@"
#!/bin/bash
cd $PEGASUS_SCRATCH_DIR
. /util/opt/lmod/lmod/init/profile
module load python/2.7 macs2
macs2 "$@"
......@@ -2,6 +2,7 @@
set -eu -o pipefail
set -o pipefail
cd $PEGASUS_SCRATCH_DIR
. /util/opt/lmod/lmod/init/profile
module load picard
......
#!/bin/bash
cd $PEGASUS_SCRATCH_DIR
. /util/opt/lmod/lmod/init/profile
module load R spp
Rscript ${SPP_NODUPS} "$@"
#!/bin/bash
cd $PEGASUS_SCRATCH_DIR
. /util/opt/lmod/lmod/init/profile
module load samtools
samtools "$@"
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