From c26ca54f7aa466df7e094516be078bdac5566043 Mon Sep 17 00:00:00 2001 From: Adam Caprez <acaprez2@unl.edu> Date: Wed, 16 Mar 2016 12:11:09 -0500 Subject: [PATCH] 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. --- chipathlon/jobs/scripts/download_fastq.py | 2 +- chipathlon/jobs/scripts/sort_wrapper.sh | 1 + chipathlon/jobs/scripts/zcat_wrapper.sh | 1 + chipathlon/jobs/wrappers/bedtools_wrapper.sh | 1 + chipathlon/jobs/wrappers/bowtie2_wrapper.sh | 1 + chipathlon/jobs/wrappers/bwa_wrapper.sh | 1 + chipathlon/jobs/wrappers/macs2_wrapper.sh | 1 + chipathlon/jobs/wrappers/picard_wrapper.sh | 1 + chipathlon/jobs/wrappers/r_spp_nodups_wrapper.sh | 1 + chipathlon/jobs/wrappers/samtools_wrapper.sh | 1 + 10 files changed, 10 insertions(+), 1 deletion(-) diff --git a/chipathlon/jobs/scripts/download_fastq.py b/chipathlon/jobs/scripts/download_fastq.py index 9b79b4b..3bd57cf 100755 --- a/chipathlon/jobs/scripts/download_fastq.py +++ b/chipathlon/jobs/scripts/download_fastq.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/bin/env python import chipathlon.utils import argparse diff --git a/chipathlon/jobs/scripts/sort_wrapper.sh b/chipathlon/jobs/scripts/sort_wrapper.sh index 87439cc..5b8ff45 100755 --- a/chipathlon/jobs/scripts/sort_wrapper.sh +++ b/chipathlon/jobs/scripts/sort_wrapper.sh @@ -1,3 +1,4 @@ #!/bin/bash +cd $PEGASUS_SCRATCH_DIR /bin/sort -k 8gr,8gr "$1" | awk 'BEGIN{OFS="\t"}{$r="PEAK_"NR; print $0;}' > "$2" diff --git a/chipathlon/jobs/scripts/zcat_wrapper.sh b/chipathlon/jobs/scripts/zcat_wrapper.sh index 5d189ed..8fc0ba4 100755 --- a/chipathlon/jobs/scripts/zcat_wrapper.sh +++ b/chipathlon/jobs/scripts/zcat_wrapper.sh @@ -1,3 +1,4 @@ #!/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" diff --git a/chipathlon/jobs/wrappers/bedtools_wrapper.sh b/chipathlon/jobs/wrappers/bedtools_wrapper.sh index bbfc47e..1cd6933 100755 --- a/chipathlon/jobs/wrappers/bedtools_wrapper.sh +++ b/chipathlon/jobs/wrappers/bedtools_wrapper.sh @@ -1,5 +1,6 @@ #!/bin/bash +cd $PEGASUS_SCRATCH_DIR . /util/opt/lmod/lmod/init/profile module load bedtools bedtools "$@" diff --git a/chipathlon/jobs/wrappers/bowtie2_wrapper.sh b/chipathlon/jobs/wrappers/bowtie2_wrapper.sh index 6a63fcb..f23550e 100755 --- a/chipathlon/jobs/wrappers/bowtie2_wrapper.sh +++ b/chipathlon/jobs/wrappers/bowtie2_wrapper.sh @@ -1,5 +1,6 @@ #!/bin/bash +cd $PEGASUS_SCRATCH_DIR . /util/opt/lmod/lmod/init/profile module load bowtie bowtie2 "$@" diff --git a/chipathlon/jobs/wrappers/bwa_wrapper.sh b/chipathlon/jobs/wrappers/bwa_wrapper.sh index 47f0780..b1b75bf 100755 --- a/chipathlon/jobs/wrappers/bwa_wrapper.sh +++ b/chipathlon/jobs/wrappers/bwa_wrapper.sh @@ -1,5 +1,6 @@ #!/bin/bash +cd $PEGASUS_SCRATCH_DIR . /util/opt/lmod/lmod/init/profile module load bwa bwa "$@" diff --git a/chipathlon/jobs/wrappers/macs2_wrapper.sh b/chipathlon/jobs/wrappers/macs2_wrapper.sh index bc3238d..cbeb384 100755 --- a/chipathlon/jobs/wrappers/macs2_wrapper.sh +++ b/chipathlon/jobs/wrappers/macs2_wrapper.sh @@ -1,5 +1,6 @@ #!/bin/bash +cd $PEGASUS_SCRATCH_DIR . /util/opt/lmod/lmod/init/profile module load python/2.7 macs2 macs2 "$@" diff --git a/chipathlon/jobs/wrappers/picard_wrapper.sh b/chipathlon/jobs/wrappers/picard_wrapper.sh index 92ffde2..b897c97 100755 --- a/chipathlon/jobs/wrappers/picard_wrapper.sh +++ b/chipathlon/jobs/wrappers/picard_wrapper.sh @@ -2,6 +2,7 @@ set -eu -o pipefail set -o pipefail +cd $PEGASUS_SCRATCH_DIR . /util/opt/lmod/lmod/init/profile module load picard diff --git a/chipathlon/jobs/wrappers/r_spp_nodups_wrapper.sh b/chipathlon/jobs/wrappers/r_spp_nodups_wrapper.sh index bf96b43..fdce742 100755 --- a/chipathlon/jobs/wrappers/r_spp_nodups_wrapper.sh +++ b/chipathlon/jobs/wrappers/r_spp_nodups_wrapper.sh @@ -1,5 +1,6 @@ #!/bin/bash +cd $PEGASUS_SCRATCH_DIR . /util/opt/lmod/lmod/init/profile module load R spp Rscript ${SPP_NODUPS} "$@" diff --git a/chipathlon/jobs/wrappers/samtools_wrapper.sh b/chipathlon/jobs/wrappers/samtools_wrapper.sh index b6cc153..7ba5f07 100755 --- a/chipathlon/jobs/wrappers/samtools_wrapper.sh +++ b/chipathlon/jobs/wrappers/samtools_wrapper.sh @@ -1,5 +1,6 @@ #!/bin/bash +cd $PEGASUS_SCRATCH_DIR . /util/opt/lmod/lmod/init/profile module load samtools samtools "$@" -- GitLab