mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-11-24 02:19:55 +00:00
64 lines
1.5 KiB
Modula-2
64 lines
1.5 KiB
Modula-2
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Bootstrap: library
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From: default/alpine:3.14.0
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%post
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# Get the actual dependencies
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apk add --no-cache ncurses libbz2 xz zlib bash
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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-$SAMTOOLS_VERSION*
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cd || exit 1
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# Cleanup build packages
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apk del --no-cache .build-deps
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%test
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test_command () {
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if ! command -v "${1}"; then
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echo "command ${1} not found!"
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export FAILED_TESTS=1
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fi
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}
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test_command bash
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test_command ps
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test_command samtools
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if [ -n "$FAILED_TESTS" ]; then
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exit 1
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fi
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%runscript
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samtools "$@"
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion 1.13
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SingularityDefinitionVersion 1
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%help
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Samtools
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========
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Samtools is a set of utilities that manipulate alignments in the SAM
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(Sequence Alignment/Map), BAM, and CRAM formats. It converts between the
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formats, does sorting, merging and indexing, and can retrieve reads in any
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regions swiftly.
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For more help, see
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- <https://www.htslib.org/doc/samtools.html>
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- <https://github.com/MillironX/singularity-builds>
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