Bootstrap: library From: default/alpine:3.14.0 %post # Part 1: Install Samtools # ======================== # Get the actual dependencies apk add --no-cache ncurses libbz2 xz zlib # Get the build dependencies apk add --no-cache --virtual .build-deps ncurses-dev musl-dev g++ make zlib-dev bzip2-dev xz-dev # Make versioning easier SAMTOOLS_VERSION='1.13' # Download the source tarball and build cd /tmp || exit 1 wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2 tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2 cd samtools-$SAMTOOLS_VERSION || exit 1 ./configure make && make install cd .. || exit 1 rm -rf samtools-$SAMTOOLS_VERSION* cd || exit 1 # Cleanup build packages apk del --no-cache .build-deps # Part 2: Install VarScan # ======================== # Install java apk add --no-cache openjdk8 # Make versioning easier VARSCAN_VERSION='v2.4.4' # Download varscan wget https://github.com/dkoboldt/varscan/raw/master/VarScan.v2.4.4.jar -O /opt/varscan.jar # Create a shim for varscan echo "#!/bin/bash" > /usr/local/bin/varscan echo "java -jar /opt/varscan.jar \"\$@\"" >> /usr/local/bin/varscan chmod +x /usr/local/bin/varscan # Part 3: Install Nextflow dependencies # ===================================== apk add --no-cache bash %test cat << "EOF" > /tmp/singularity-test.sh #!/bin/bash CMDS=('bash' 'ps' 'java' 'varscan' 'samtools') for CMD in "${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 2 %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 - -