95 lines
2.0 KiB
Nix
95 lines
2.0 KiB
Nix
{
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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,
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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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nix-update-script,
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}:
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buildPythonPackage rec {
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pname = "pysam";
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version = "0.23.3";
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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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tag = "v${version}";
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hash = "sha256-yOLnfuGQW+j0nHy4MRlwurZMpeRHTGmQ9eLmihcAGoQ=";
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};
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build-system = [
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cython
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setuptools
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];
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nativeBuildInputs = [
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samtools
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];
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buildInputs = [
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bzip2
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curl
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libdeflate
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xz
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zlib
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];
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# Use nixpkgs' htslib instead of the bundled one
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# See https://pysam.readthedocs.io/en/latest/installation.html#external
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# NOTE that htslib should be version compatible with pysam
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preBuild = ''
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export HTSLIB_MODE=shared
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export HTSLIB_LIBRARY_DIR=${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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"pysam.libcsamtools"
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];
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passthru.updateScript = nix-update-script { };
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meta = {
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description = "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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changelog = "https://github.com/pysam-developers/pysam/releases/tag/${src.tag}";
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homepage = "https://pysam.readthedocs.io";
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maintainers = with lib.maintainers; [ unode ];
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license = lib.licenses.mit;
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platforms = lib.platforms.unix;
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};
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}
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