refactor: use bin/redirect from xavier

bin/carlisle

@@ -0,0 +1 @@
+redirect

bin/redirect

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+#!/usr/bin/env bash
+# This is a wrapper for the pipeline script
+# It:
+# - loads require modules and conda environments
+# - parses the variables directly to the python script
+
+SCRIPTDIRNAME=$(readlink -f $(dirname "$BASH_SOURCE"))
+
+# add "bin" to PATH
+if [[ ":$PATH:" != *":${SCRIPTDIRNAME}:"* ]];then
+	export PATH=${PATH}:${SCRIPTDIRNAME}
+fi
+
+TOOLDIR=$(dirname "$SCRIPTDIRNAME")
+
+# find out if you are running on biowulf or frce
+hpc_name=$(scontrol show config | grep ClusterName | sed "s/^.*= //")
+# load conda
+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
+# 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
+
+${TOOLDIR}/main.py "$@" || true