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What happens if I push all of nixpkgs
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1.7 kB · 80 lines
Nix
at litex
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buildPythonPackage rec { pname = "pysam"; version = "0.21.0";
# Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is # missing some files which cause test failures. # Tracked at: https://github.com/pysam-developers/pysam/issues/616 src = fetchFromGitHub { owner = "pysam-developers"; repo = "pysam"; rev = "refs/tags/v${version}"; hash = "sha256-C4/AJwcUyLoUEUEnsATLHJb5F8mltP8X2XfktYu0OTo="; };
nativeBuildInputs = [ samtools ];
buildInputs = [ bzip2 curl libdeflate xz zlib ];
propagatedBuildInputs = [ cython ];
# Use nixpkgs' htslib instead of the bundled one # See https://pysam.readthedocs.io/en/latest/installation.html#external # NOTE that htslib should be version compatible with pysam preBuild = '' export HTSLIB_MODE=shared export HTSLIB_LIBRARY_DIR=${htslib}/lib export HTSLIB_INCLUDE_DIR=${htslib}/include '';
nativeCheckInputs = [ pytestCheckHook bcftools htslib ];
preCheck = '' export HOME=$TMPDIR make -C tests/pysam_data make -C tests/cbcf_data make -C tests/tabix_data rm -rf pysam '';
pythonImportsCheck = [ "pysam" "pysam.bcftools" "pysam.libchtslib" "pysam.libcutils" "pysam.libcvcf" ];
meta = with lib; { description = "A python module for reading, manipulating and writing genome data sets"; homepage = "https://pysam.readthedocs.io/"; maintainers = with maintainers; [ unode ]; license = licenses.mit; platforms = platforms.unix; };}