mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-11-01 00:23:10 +00:00
75 lines
1.7 KiB
Modula-2
75 lines
1.7 KiB
Modula-2
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Bootstrap: library
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From: millironx/default/samtools:1.13
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%post
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# Get the actual dependencies
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apk add --no-cache perl
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# Get the build dependencies
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apk add --no-cache --virtual .build-deps musl-dev g++ make zlib-dev
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# Part 1: Install minimap2
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# ========================
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# Make versioning easier
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MINIMAP2_VERSION='2.22'
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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/lh3/minimap2/releases/download/v$MINIMAP2_VERSION/minimap2-$MINIMAP2_VERSION.tar.bz2
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tar xjvf minimap2-$MINIMAP2_VERSION.tar.bz2
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cd minimap2-$MINIMAP2_VERSION || exit 1
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make
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install -D -m 0755 minimap2 -t /usr/bin
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cd .. || exit 1
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rm -rf minimap2-$MINIMAP2_VERSION*
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cd || exit 1
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# Part 2: Install samclip
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SAMCLIP_VERSION='0.4.0'
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cd /usr/bin || exit 1
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wget https://raw.githubusercontent.com/tseemann/samclip/v$SAMCLIP_VERSION/samclip
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chmod a+x samclip
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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 ${1} not found!"
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export FAILED_TESTS=1
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fi
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}
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test_command bash
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test_command ps
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test_command samtools
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test_command minimap2
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test_command samclip
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if [ -n "$FAILED_TESTS" ]; then
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exit 1
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fi
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%runscript
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minimap2 "$@"
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion 2.22
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SingularityDefinitionVersion 1
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%help
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minimap2
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========
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Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA
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sequences against a large reference database.
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For more help, see
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- <https://lh3.github.io/minimap2/>
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- <https://github.com/lh3/minimap2>
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- <https://github.com/MillironX/singularity-builds>
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