Skip to content

Instantly share code, notes, and snippets.

@clintval

clintval/compile-nf-groovy.sh

Created January 8, 2024 16:41
Show Gist options
  • Save clintval/55ee8d6ddb3b70c8dab175b8aa3c69ba to your computer and use it in GitHub Desktop.
Save clintval/55ee8d6ddb3b70c8dab175b8aa3c69ba to your computer and use it in GitHub Desktop.
Download ZIP
Compile Nextflow library groovy code linked against Nextflow
Raw
compile-nf-groovy.sh
#!/bin/bash
# Attempts to compile the groovy present in nextflow/lib/ with the groovy compiler and nextflow
# libararies properly linked (because they dont live in a place groovy can find them by default.)
#
# Must have a conda env with nextflow and groovy installed in order for this script to work.
SCRIPT_DIR=$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )
NEXTFLOW_CLASSPATH_STRING="."
while IFS= read -r -d '' jar
do
NEXTFLOW_CLASSPATH_STRING="$NEXTFLOW_CLASSPATH_STRING:$jar"
done < <(find ${CONDA_PREFIX}/share/nextflow -name '*.jar' -print0)
export NEXTFLOW_CLASSPATH_STRING
mkdir -p "${SCRIPT_DIR}/classes/"
groovyc \
--classpath "${NEXTFLOW_CLASSPATH_STRING}" \
-d "${SCRIPT_DIR}/classes/" \
"${SCRIPT_DIR}/../nextflow/lib/"*.groovy
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment