Merge pull request #111 from CCBR/redirect

refactor: update bin/redirect from RENEE

CHANGELOG.md

@@ -10,6 +10,7 @@
 - Increased memory for rules: BWA mem, qualimap, kraken. gatk_contamination is not localrule. (#89, @samarth8392)
 - Added new human test dataset for github workflow (#27, @samarth8392)
 - fixes minor bug in GUI related to choosing the correct default target file (#108, @samarth8392)
+- Fix bug in the driver script that caused the snakemake module not to be loaded on biowulf in some cases. (#111, @kelly-sovacool)
 
 ## XAVIER 3.0.3
 

bin/redirect

@@ -1,43 +1,26 @@
 #!/usr/bin/env bash
-
-# This is a wrapper for spook python script
+# This is a wrapper for the pipeline script
 # It:
-# - loads require modules
+# - loads require modules and conda environments
 # - parses the variables directly to the python script
 
-
-function load_module_if_needed {
-	module_name=$1
-	x=$(type -P $module_name)
-	if [[ -z $x ]];then
-		module load $module_name
-	fi
-}
-
-SCRIPTNAME="$BASH_SOURCE"
-SCRIPTDIRNAME=$(readlink -f $(dirname "$SCRIPTNAME"))
+SCRIPTDIRNAME=$(readlink -f $(dirname "$BASH_SOURCE"))
 
 # add "bin" to PATH
 if [[ ":$PATH:" != *":${SCRIPTDIRNAME}:"* ]];then
 	export PATH=${PATH}:${SCRIPTDIRNAME}
 fi
 
 TOOLDIR=$(dirname "$SCRIPTDIRNAME")
-TOOLNAME=$(basename "$SCRIPTNAME")
-# echo $TOOLNAME
 
 # find out if you are running on biowulf or frce
-nbiowulf=$(scontrol show config | grep -i -c biowulf)
-if [[ "$nbiowulf" > 0 ]];then ISBIOWULF=true; else ISBIOWULF=false;fi
-nfrce=$(scontrol show config | grep -i -c fsitgl)
-if [[ "$nfrce" > 0 ]];then ISFRCE=true; else ISFRCE=false;fi
-
+hpc_name=$(scontrol show config | grep ClusterName | sed "s/^.*= //")
 # load conda
-if [[ $ISBIOWULF == true ]];then
-       . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
+if [[ $hpc_name == biowulf ]]; then
+	. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
 	conda activate py311
-elif [[ $ISFRCE == true ]];then
-       . "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh"
+elif [[ $hpc_name == fnlcr ]]; then
+	. "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh"
 	conda activate py311
 else
 	echo "You are NOT running on BIOWULF or on FRCE"
@@ -55,13 +38,12 @@ fi
 #   - singularity
 #   - snakemake
 # are in PATH
-if [[ $ISBIOWULF == true ]];then
-	load_module_if_needed singularity
-	load_module_if_needed snakemake/7
-elif [[ $ISFRCE == true ]];then
-# snakemake module on FRCE does not work as expected
-# use the conda installed version of snakemake instead
-	load_module_if_needed load singularity
+if [[ $hpc_name == biowulf ]];then
+	module load singularity snakemake/7
+elif [[ $hpc_name == fnlcr ]];then
+	# snakemake module on FRCE does not work as expected
+	# use the conda installed version of snakemake instead
+	module load singularity
 	export PATH="/mnt/projects/CCBR-Pipelines/bin:$PATH"
 fi