mirror of
https://github.com/MillironX/singularity-builds.git
synced 2024-11-22 01:46:04 +00:00
72 lines
1.8 KiB
Modula-2
72 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>
|