updated LSF run-pipe.sh to use same dotkits as UGER run-pipe.sh

broadinstitute · Feb 12, 2016 · 6099cd7 · 6099cd7
1 parent 67471aa
commit 6099cd7
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Showing 3 changed files with 2 additions and 5 deletions.
diff --git a/pipes/Broad_LSF/run-pipe.sh b/pipes/Broad_LSF/run-pipe.sh
@@ -2,10 +2,7 @@
 # Wrappers around Snakemake for use on the Broad LSF cluster
 
 # load necessary Broad dotkits
-eval `/broad/software/dotkit/init -b`
-reuse -q LSF
-reuse -q Python-3.4
-reuse -q Perl-5.10
+source "$BINDIR/pipes/Broad_common/setup_dotkits.sh"
 
 # load config dirs from config.yaml
 VENVDIR=`python -c 'import yaml;f=open("config.yaml");print(yaml.safe_load(f)["venv_dir"]);f.close()'`

diff --git a/pipes/Broad_UGER/run-pipe.sh b/pipes/Broad_UGER/run-pipe.sh
@@ -5,7 +5,7 @@
 VENVDIR=`python -c 'import yaml; import os; f=open("config.yaml");print(os.path.realpath(yaml.safe_load(f)["venv_dir"]));f.close()'`
 BINDIR=`python -c 'import yaml; import os; f=open("config.yaml");print(os.path.realpath(yaml.safe_load(f)["bin_dir"]));f.close()'`
 
-source "$BINDIR/pipes/Broad_UGER/setup_dotkits.sh"
+source "$BINDIR/pipes/Broad_common/setup_dotkits.sh"
 
 # load Python virtual environment
 source "$VENVDIR/bin/activate"

diff --git a/pipes/Broad_UGER/setup_dotkits.sh → pipes/Broad_common/setup_dotkits.sh b/pipes/Broad_UGER/setup_dotkits.sh → pipes/Broad_common/setup_dotkits.sh