refactor: update bin/redirect from xavier

bin/redirect

@@ -1,39 +1,50 @@
 #!/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
 
-SCRIPTNAME="$0"
-SCRIPTDIRNAME=$(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
+hpc_name=$(scontrol show config | grep ClusterName | sed "s/^.*= //")
 # load conda
-# if [[ "$HOSTNAME" == "biowulf.nih.gov" ]];then
-#       . "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
-# elif [[ "$HOSTNAME" == "fsitgl-head01p.ncifcrf.gov" ]];then
-#       . "/mnt/projects/CCBR-Pipelines/resources/miniconda3/etc/profile.d/conda.sh"
-# fi
-# conda activate py311
+if [[ $hpc_name == biowulf ]]; then
+	. "/data/CCBR_Pipeliner/db/PipeDB/Conda/etc/profile.d/conda.sh"
+	conda activate py311
+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"
+	echo "Please make sure that:"
+	echo "  - py311 conda environment is activated"
+	echo "  - singularity is in PATH"
+	echo "  - snakemake is in PATH"
+fi
+# if not on biowulf or frce then
+# use py311.environment.yml in resources folder to create the py311 conda environment
+# and load py311
 
 # load required modules
-# module purge
-# module load singularity
-# if [[ "$HOSTNAME" == "biowulf.nih.gov" ]];then
-# 	module load snakemake
-# elif [[ "$HOSTNAME" == "fsitgl-head01p.ncifcrf.gov" ]];then
-# # snakemake module on FRCE does not work as expected
-# # use the conda installed version of snakemake instead
-# 	export PATH="/mnt/projects/CCBR-Pipelines/bin:$PATH"
-# fi
+# if running somewhere other than biowulf or frce, then ensure that
+#   - singularity
+#   - snakemake
+# are in PATH
+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
 
-${TOOLDIR}/${TOOLNAME} "$@" || true
+${TOOLDIR}/aspen "$@" || true