1 files changed, 48 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/development/python-modules/pysam/default.nix b/nixpkgs/pkgs/development/python-modules/pysam/default.nix
new file mode 100644
index 000000000000..05f2db8ac063
--- /dev/null
+++ b/nixpkgs/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 = "0.15.2";
+
+  # 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${version}";
+    sha256 = "03aczbzx6gmvgy60fhswpwkry7a8zb5q1pbp55v5gx8hk15n40k1";
+  };
+
+  buildInputs = [ bzip2 curl cython lzma zlib ];
+
+  checkInputs = [ pytest bcftools htslib samtools ];
+
+  checkPhase = "py.test";
+
+  preInstall = ''
+    export HOME=$(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" ];
+  };
+}