mirror of
https://github.com/MillironX/singularity-builds.git
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63 lines
1.5 KiB
Modula-2
63 lines
1.5 KiB
Modula-2
Bootstrap: library
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From: default/alpine:3.14.0
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%post
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# Declare version variable
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export SNIFFLES_VERSION='1.0.12'
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export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"
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# Install build dependencies
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apk add --no-cache --virtual .build-deps \
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git cmake make gcc g++ zlib-dev
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# Install real dependencies
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apk add --no-cache bash
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# Get Sniffles
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cd /opt || exit 1
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git clone https://github.com/fritzsedlazeck/Sniffles.git
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cd Sniffles || exit 1
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git checkout $SNIFFLES_TAG
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# Build Sniffles
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mkdir build && cd build || exit 1
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cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/usr/local
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make
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# Add Sniffles to PATH
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export PATH=/opt/Sniffles/bin/sniffles-core-$SNIFFLES_VERSION:$PATH
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# Cleanup packages
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apk del --no-cache .build-deps
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%environment
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export SNIFFLES_VERSION='1.0.12'
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export SNIFFLES_TAG="v${SNIFFLES_VERSION}b"
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export PATH=/opt/Sniffles/bin/sniffles-core-$SNIFFLES_VERSION:$PATH
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%test
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command -v bash
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command -v ps
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command -v sniffles
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command -v sniffles-debug
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%runscript
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sniffles "$@"
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion v1.0.12b
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SingularityDefinitionVersion 2
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%help
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Sniffles
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========
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Sniffles is a structural variation caller using third generation sequencing
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(PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using
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evidence from split-read alignments, high-mismatch regions, and coverage
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analysis.
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For more help, see
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- <https://github.com/fritzsedlazeck/Sniffles>
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- <https://github.com/MillironX/singularity-builds>
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