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author | Renato Alves <alves.rjc@gmail.com> | 2020-02-17 16:22:13 +0100 |
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committer | Renato Alves <alves.rjc@gmail.com> | 2020-02-21 10:12:32 +0100 |
commit | bf88bf47d1976b396fb06c5e608bb68e879e6952 (patch) | |
tree | e66c53aba05e43d84e4d764ec6e5f96b6602f86f /pkgs/development | |
parent | 0591e947571ccb8fec02524c1e27de4bc858b8d9 (diff) | |
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pysam: 0.15.3 -> 0.15.4
Also disable tests until upstream test data issues are resolved. See link in comment in code for more information.
Diffstat (limited to 'pkgs/development')
-rw-r--r-- | pkgs/development/python-modules/pysam/default.nix | 27 |
1 files changed, 18 insertions, 9 deletions
diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix index 46dd54c62e20..38b55c4563da 100644 --- a/pkgs/development/python-modules/pysam/default.nix +++ b/pkgs/development/python-modules/pysam/default.nix @@ -14,7 +14,7 @@ buildPythonPackage rec { 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 # missing some files which cause test failures. @@ -23,26 +23,35 @@ buildPythonPackage rec { owner = "pysam-developers"; repo = "pysam"; rev = "v${version}"; - sha256 = "0g6md20gsr24pdr9b8nj403w31ixfjv8bjhdvg3x476kjiq1kvyb"; + sha256 = "04w6h6mv6lsr74hj9gy4r2laifcbhgl2bjcr4r1l9r73xdd45mdy"; }; + nativeBuildInputs = [ samtools ]; buildInputs = [ bzip2 curl cython lzma zlib ]; - checkInputs = [ pytest bcftools htslib samtools ]; - + checkInputs = [ pytest bcftools htslib ]; checkPhase = "py.test"; - preInstall = '' + # tests require samtools<=1.9 + doCheck = false; + preCheck = '' export HOME=$(mktemp -d) make -C tests/pysam_data make -C tests/cbcf_data ''; - meta = { - homepage = https://pysam.readthedocs.io/; + pythonImportsCheck = [ + "pysam" + "pysam.bcftools" + "pysam.libcutils" + "pysam.libcvcf" + ]; + + meta = with lib; { description = "A python module for reading, manipulating and writing genome data sets"; - maintainers = with lib.maintainers; [ unode ]; - license = lib.licenses.mit; + homepage = "https://pysam.readthedocs.io/"; + maintainers = with maintainers; [ unode ]; + license = licenses.mit; platforms = [ "i686-linux" "x86_64-linux" ]; }; } |