quote symlink paths, change conda path used for "source activate"

broadinstitute · Jul 12, 2016 · bc92aac · bc92aac
1 parent 6e8a6e9
commit bc92aac
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Showing 4 changed files with 8 additions and 8 deletions.
diff --git a/easy-deploy-script/easy-deploy-viral-ngs.sh b/easy-deploy-script/easy-deploy-viral-ngs.sh
@@ -177,11 +177,11 @@ function create_project(){
     touch samples-runs.txt
     touch samples-assembly-failures.txt
     cp $VIRAL_NGS_PATH/pipes/config.yaml ../../$VIRAL_NGS_DIR/pipes/Snakefile ./
-    ln -s $VIRAL_NGS_PATH/ $(pwd)/bin
-    ln -s $VIRAL_CONDA_ENV_PATH/ $(pwd)/venv
-    ln -s $MINICONDA_PATH/ $(pwd)/mc3
-    ln -s $VIRAL_NGS_PATH/pipes/Broad_UGER/run-pipe.sh $(pwd)/run-pipe_UGER.sh
-    ln -s $VIRAL_NGS_PATH/pipes/Broad_LSF/run-pipe.sh $(pwd)/run-pipe_LSF.sh
+    ln -s "$VIRAL_NGS_PATH/" "$(pwd)/bin"
+    ln -s "$VIRAL_CONDA_ENV_PATH/" "$(pwd)/conda-env"
+    ln -s "$MINICONDA_PATH/" "$(pwd)/mc3"
+    ln -s "$VIRAL_NGS_PATH/pipes/Broad_UGER/run-pipe.sh" "$(pwd)/run-pipe_UGER.sh"
+    ln -s "$VIRAL_NGS_PATH/pipes/Broad_LSF/run-pipe.sh" "$(pwd)/run-pipe_LSF.sh"
 
     cd $starting_dir
 }

diff --git a/pipes/Broad_LSF/run-pipe.sh b/pipes/Broad_LSF/run-pipe.sh
@@ -19,7 +19,7 @@ unuse  Python-3.4
 export PATH="$MINICONDADIR/bin:$PATH"
 
 # load conda environment
-source activate "$CONDAENVDIR/bin"
+source activate "$CONDAENVDIR"
 
 # invoke Snakemake in cluster mode with custom wrapper scripts
 snakemake --timestamp --rerun-incomplete --keep-going --nolock \

diff --git a/pipes/Broad_UGER/jobscript.sh b/pipes/Broad_UGER/jobscript.sh
@@ -13,7 +13,7 @@ unuse Python-3.4
 export PATH="$MINICONDADIR/bin:$PATH"
 
 # load Python virtual environment
-source activate "$CONDAENVDIR/bin"
+source activate "$CONDAENVDIR"
 
 # if listing the data directory fails, exit 99 to reschedule the job
 # since the node with the job doesn't have the NFS share mounted.

diff --git a/pipes/Broad_UGER/run-pipe.sh b/pipes/Broad_UGER/run-pipe.sh
@@ -19,7 +19,7 @@ unuse  Python-3.4
 export PATH="$MINICONDADIR/bin:$PATH"
 
 # load conda environment
-source activate "$CONDAENVDIR/bin"
+source activate "$CONDAENVDIR"
 
 # invoke Snakemake in cluster mode with custom wrapper scripts
 snakemake --timestamp --rerun-incomplete --keep-going --nolock \