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72 lines
1.8 KiB
Modula-2
72 lines
1.8 KiB
Modula-2
Bootstrap: library
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From: millironx/default/htslib:1.13
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%post
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# Install dependencies
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apk add --no-cache python3 libcurl
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# Install build dependencies
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apk add --no-cache --virtual .build-deps py-pip g++ musl-dev make python3-dev boost-dev curl-dev
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# Install python package dependencies
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pip install --no-cache-dir biopython==1.79 numpy==1.21.2
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# Make versioning easier
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SHORAH_VERSION=1.99.2
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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/cbg-ethz/shorah/releases/download/v$SHORAH_VERSION/shorah-$SHORAH_VERSION.tar.bz2 -O shorah-$SHORAH_VERSION.tar.bz2
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tar xjvf shorah-$SHORAH_VERSION.tar.bz2
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cd shorah-$SHORAH_VERSION
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./configure
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make
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make install
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cd .. || exit 1
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rm -rf shorah-$SHORAH_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 ${1} not found!"
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export FAILED_TESTS=1
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fi
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}
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test_command bash
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test_command ps
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test_command shorah
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test_command b2w
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test_command diri_sampler
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test_command fil
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if [ -n "$FAILED_TESTS" ]; then
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exit 1
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fi
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%runscript
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shorah "$@"
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%labels
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Author 25492070+MillironX@users.noreply.github.com
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SoftwareVersion 2.0.2
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SingularityDefinitionVersion 1
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%help
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ShoRAH
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======
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ShoRAH is an open source project for the analysis of next generation
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sequencing data. It is designed to analyse genetically heterogeneous samples.
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Its tools are written in different programming languages and provide error
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correction, haplotype reconstruction and estimation of the frequency of the
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different genetic variants present in a mixed sample.
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For more help, see
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- <http://cbg-ethz.github.io/shorah>
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- <https://github.com/MillironX/singularity-builds>
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