singularity-builds/shorah/shorah.def

71 lines
1.8 KiB
Modula-2

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