2018-02-02 01:24:06 +00:00
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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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, 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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2019-01-27 14:47:36 +00:00
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version = "0.15.2";
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2018-02-02 01:24:06 +00:00
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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${version}";
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2019-01-27 14:47:36 +00:00
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sha256 = "03aczbzx6gmvgy60fhswpwkry7a8zb5q1pbp55v5gx8hk15n40k1";
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2018-02-02 01:24:06 +00:00
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};
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buildInputs = [ bzip2 curl cython lzma zlib ];
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checkInputs = [ pytest bcftools htslib samtools ];
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checkPhase = "py.test";
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preInstall = ''
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export HOME=$(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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meta = {
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homepage = http://pysam.readthedocs.io/;
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description = "A python module for reading, manipulating and writing genome data sets";
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maintainers = with lib.maintainers; [ unode ];
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license = lib.licenses.mit;
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platforms = [ "i686-linux" "x86_64-linux" ];
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};
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}
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