diff --git a/pkgs/development/python-modules/pysam/default.nix b/pkgs/development/python-modules/pysam/default.nix new file mode 100644 index 00000000000..9d6cbacc958 --- /dev/null +++ b/pkgs/development/python-modules/pysam/default.nix @@ -0,0 +1,48 @@ +{ lib +, buildPythonPackage +, fetchFromGitHub +, bzip2 +, bcftools +, curl +, cython +, htslib +, lzma +, pytest +, samtools +, zlib +}: + +buildPythonPackage rec { + pname = "pysam"; + version = "0.13.0"; + + # Fetching from GitHub instead of PyPi cause the 0.13 src release on PyPi is + # missing some files which cause test failures. + # Tracked at: https://github.com/pysam-developers/pysam/issues/616 + src = fetchFromGitHub { + owner = "pysam-developers"; + repo = "pysam"; + rev = "v${version}"; + sha256 = "1lwbcl38w1x0gciw5psjp87msmv9zzkgiqikg9b83dqaw2y5az1i"; + }; + + buildInputs = [ bzip2 curl cython lzma zlib ]; + + checkInputs = [ pytest bcftools htslib samtools ]; + + checkPhase = "py.test"; + + preInstall = '' + export HOME=$(mktemp -d) + make -C tests/pysam_data + make -C tests/cbcf_data + ''; + + meta = { + homepage = http://pysam.readthedocs.io/; + description = "A python module for reading, manipulating and writing genome data sets"; + maintainers = with lib.maintainers; [ unode ]; + license = lib.licenses.mit; + platforms = [ "i686-linux" "x86_64-linux" ]; + }; +} diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix index 7a279d96591..0bb304ced4b 100644 --- a/pkgs/top-level/python-packages.nix +++ b/pkgs/top-level/python-packages.nix @@ -13226,6 +13226,8 @@ in { }; }; + pysam = callPackage ../development/python-modules/pysam { }; + pysaml2 = buildPythonPackage rec { name = "pysaml2-${version}"; version = "3.0.2";