85 lines
1.8 KiB
Nix
85 lines
1.8 KiB
Nix
{ lib
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, buildPythonPackage
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, fetchFromGitHub
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, bzip2
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, bcftools
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, curl
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, cython_3
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, htslib
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, libdeflate
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, xz
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, pytestCheckHook
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, setuptools
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, samtools
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, zlib
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}:
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buildPythonPackage rec {
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pname = "pysam";
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version = "0.22.0";
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pyproject = true;
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# Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
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# missing some files which cause test failures.
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# Tracked at: https://github.com/pysam-developers/pysam/issues/616
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src = fetchFromGitHub {
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owner = "pysam-developers";
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repo = "pysam";
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rev = "refs/tags/v${version}";
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hash = "sha256-TLqZF5NS9ROH8z7c2ZxfOYNRIe5pabMNBuhQ4azFmDU=";
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};
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nativeBuildInputs = [
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cython_3
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samtools
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setuptools
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];
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buildInputs = [
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bzip2
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curl
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libdeflate
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xz
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zlib
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];
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# Use nixpkgs' htslib instead of the bundled one
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# See https://pysam.readthedocs.io/en/latest/installation.html#external
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# NOTE that htslib should be version compatible with pysam
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preBuild = ''
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export HTSLIB_MODE=shared
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export HTSLIB_LIBRARY_DIR=${htslib}/lib
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export HTSLIB_INCLUDE_DIR=${htslib}/include
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'';
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nativeCheckInputs = [
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pytestCheckHook
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bcftools
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htslib
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];
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preCheck = ''
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export HOME=$TMPDIR
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make -C tests/pysam_data
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make -C tests/cbcf_data
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make -C tests/tabix_data
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rm -rf pysam
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'';
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pythonImportsCheck = [
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"pysam"
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"pysam.bcftools"
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"pysam.libchtslib"
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"pysam.libcutils"
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"pysam.libcvcf"
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];
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meta = with lib; {
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description = "A python module for reading, manipulating and writing genome data sets";
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downloadPage = "https://github.com/pysam-developers/pysam";
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homepage = "https://pysam.readthedocs.io/";
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maintainers = with maintainers; [ unode ];
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license = licenses.mit;
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platforms = platforms.unix;
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};
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}
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