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 = "0.16.0.1";
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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${version}";
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sha256 = "168bwwm8c2k22m7paip8q0yajyl7xdxgnik0bgjl7rhqg0majz0f";
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};
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nativeBuildInputs = [ samtools ];
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buildInputs = [ bzip2 curl cython lzma zlib ];
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checkInputs = [ pytest bcftools htslib ];
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checkPhase = "py.test";
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# tests require samtools<=1.9
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doCheck = false;
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preCheck = ''
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export HOME=$(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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