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94 lines
2.6 KiB
Modula-2
94 lines
2.6 KiB
Modula-2
Bootstrap: library
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From: default/alpine:3.14.0
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%post
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# Part 1: Install Samtools
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# ========================
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# Get the actual dependencies
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apk add --no-cache ncurses libbz2 xz zlib
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# Get the build dependencies
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apk add --no-cache --virtual .build-deps ncurses-dev musl-dev g++ make zlib-dev bzip2-dev xz-dev
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# Make versioning easier
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SAMTOOLS_VERSION='1.13'
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# Download the source tarball and build
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cd /tmp || exit 1
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wget https://github.com/samtools/samtools/releases/download/$SAMTOOLS_VERSION/samtools-$SAMTOOLS_VERSION.tar.bz2
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tar xjvf samtools-$SAMTOOLS_VERSION.tar.bz2
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cd samtools-$SAMTOOLS_VERSION || exit 1
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./configure
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make && make install
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cd .. || exit 1
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rm -rf samtools-$SAMTOOLS_VERSION*
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cd || exit 1
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# Cleanup build packages
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apk del --no-cache .build-deps
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# Part 2: Install VarScan
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# ========================
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# Install java
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apk add --no-cache openjdk8
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# Make versioning easier
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VARSCAN_VERSION='v2.4.4'
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# Download varscan
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wget https://github.com/dkoboldt/varscan/raw/master/VarScan.v2.4.4.jar -O /opt/varscan.jar
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# Create a shim for varscan
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echo "#!/bin/bash" > /usr/local/bin/varscan
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echo "java -jar /opt/varscan.jar \"\$@\"" >> /usr/local/bin/varscan
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chmod +x /usr/local/bin/varscan
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# Part 3: Install Nextflow dependencies
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# =====================================
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apk add --no-cache bash
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%test
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cat << "EOF" > /tmp/singularity-test.sh
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#!/bin/bash
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CMDS=('bash' 'ps' 'java' 'varscan' 'samtools')
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for CMD in "${CMDS[@]}"; do
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if ! command -v "$CMD"; then
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echo "command $CMD not found!"
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FAILED_TESTS=1
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fi
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done
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# Abort if a test failed
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if [ -n "$FAILED_TESTS" ]; then
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exit 1
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fi
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EOF
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chmod +x /tmp/singularity-test.sh
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bash /tmp/singularity-test.sh
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%runscript
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varscan "$@"
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion v2.4.4
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SingularityDefinitionVersion 2
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%help
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VarScan
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=======
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VarScan is a platform-independent mutation caller for targeted, exome, and
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whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM,
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Roche/454, and similar instruments. It can be used to detect different types
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of variation:
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- Germline variants (SNPs an dindels) in individual samples or pools of samples.
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- Multi-sample variants (shared or private) in multi-sample datasets (with mpileup).
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- Somatic mutations, LOH events, and germline variants in tumor-normal pairs.
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- Somatic copy number alterations (CNAs) in tumor-normal exome data.
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For more help, see
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- <https://dkoboldt.github.io/varscan/>
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- <https://github.com/MillironX/singularity-builds>
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