diff --git a/varscan/varscan.def b/varscan/varscan.def new file mode 100644 index 0000000..c33f749 --- /dev/null +++ b/varscan/varscan.def @@ -0,0 +1,60 @@ +Bootstrap: library +From: default/alpine:3.14.0 + +%post + # Install java and bash (for Nextflow) + apk add --no-cache openjdk8 bash + + # Make versioning easier + VARSCAN_VERSION='v2.4.4' + + # Download varscan + wget https://github.com/dkoboldt/varscan/raw/master/VarScan.v2.4.4.jar -O /opt/varscan.jar + + # Create a shim for varscan + echo "#!/bin/bash" > /usr/local/bin/varscan + echo "java -jar /opt/varscan.jar \"\$@\"" >> /usr/local/bin/varscan + chmod +x /usr/local/bin/varscan + +%test + cat << "EOF" > /tmp/singularity-test.sh + #!/bin/bash + CMDS=('bash' 'ps' 'java' 'varscan') + for CMD in "${CMDS[@]}"; do + if ! command -v "$CMD"; then + echo "command $CMD not found!" + FAILED_TESTS=1 + fi + done + # Abort if a test failed + if [ -n "$FAILED_TESTS" ]; then + exit 1 + fi + EOF + chmod +x /tmp/singularity-test.sh + bash /tmp/singularity-test.sh + +%runscript + varscan "$@" + +%labels + Author 25492070+MillironX@users.noreply.github.com + SoftwareVersion v2.4.4 + SingularityDefinitionVersion 1 + +%help + VarScan + ======= + + VarScan is a platform-independent mutation caller for targeted, exome, and + whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, + Roche/454, and similar instruments. It can be used to detect different types + of variation: + - Germline variants (SNPs an dindels) in individual samples or pools of samples. + - Multi-sample variants (shared or private) in multi-sample datasets (with mpileup). + - Somatic mutations, LOH events, and germline variants in tumor-normal pairs. + - Somatic copy number alterations (CNAs) in tumor-normal exome data. + + For more help, see + - + -