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https://github.com/CHN-beta/nixpkgs.git
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07f20d0624
Also disable tests until upstream test data issues are resolved.
See link in comment in code for more information.
(cherry picked from commit bf88bf47d1)
58 lines
1.3 KiB
Nix
58 lines
1.3 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
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, htslib
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, lzma
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, pytest
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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 = "0.15.4";
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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 = "v${version}";
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sha256 = "04w6h6mv6lsr74hj9gy4r2laifcbhgl2bjcr4r1l9r73xdd45mdy";
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};
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nativeBuildInputs = [ samtools ];
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buildInputs = [ bzip2 curl cython lzma zlib ];
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checkInputs = [ pytest bcftools htslib ];
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checkPhase = "py.test";
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# tests require samtools<=1.9
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doCheck = false;
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preCheck = ''
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export HOME=$(mktemp -d)
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make -C tests/pysam_data
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make -C tests/cbcf_data
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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.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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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 = [ "i686-linux" "x86_64-linux" ];
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};
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}
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