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pysam: 0.15.3 -> 0.15.4

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Also disable tests until upstream test data issues are resolved.
See link in comment in code for more information.
This commit is contained in:
Renato Alves 2020-02-17 16:22:13 +01:00
parent 0591e94757
commit bf88bf47d1
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1 changed files with 18 additions and 9 deletions
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27
pkgs/development/python-modules/pysam/default.nix
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@ -14,7 +14,7 @@
buildPythonPackage rec { buildPythonPackage rec {
pname = "pysam"; pname = "pysam";
version = "0.15.3"; version = "0.15.4";
# Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is
# missing some files which cause test failures. # missing some files which cause test failures.
@ -23,26 +23,35 @@ buildPythonPackage rec {
owner = "pysam-developers"; owner = "pysam-developers";
repo = "pysam"; repo = "pysam";
rev = "v${version}"; rev = "v${version}";
sha256 = "0g6md20gsr24pdr9b8nj403w31ixfjv8bjhdvg3x476kjiq1kvyb"; sha256 = "04w6h6mv6lsr74hj9gy4r2laifcbhgl2bjcr4r1l9r73xdd45mdy";
}; };
nativeBuildInputs = [ samtools ];
buildInputs = [ bzip2 curl cython lzma zlib ]; buildInputs = [ bzip2 curl cython lzma zlib ];
checkInputs = [ pytest bcftools htslib samtools ]; checkInputs = [ pytest bcftools htslib ];
checkPhase = "py.test"; checkPhase = "py.test";
preInstall = '' # tests require samtools<=1.9
doCheck = false;
preCheck = ''
export HOME=$(mktemp -d) export HOME=$(mktemp -d)
make -C tests/pysam_data make -C tests/pysam_data
make -C tests/cbcf_data make -C tests/cbcf_data
''; '';
meta = { pythonImportsCheck = [
homepage = https://pysam.readthedocs.io/; "pysam"
"pysam.bcftools"
"pysam.libcutils"
"pysam.libcvcf"
];
meta = with lib; {
description = "A python module for reading, manipulating and writing genome data sets"; description = "A python module for reading, manipulating and writing genome data sets";
maintainers = with lib.maintainers; [ unode ]; homepage = "https://pysam.readthedocs.io/";
license = lib.licenses.mit; maintainers = with maintainers; [ unode ];
license = licenses.mit;
platforms = [ "i686-linux" "x86_64-linux" ]; platforms = [ "i686-linux" "x86_64-linux" ];
}; };
} }