Merge pull request #98283 from risicle/ris-truvari-2.0.2

truvari: 1.3.4 -> 2.0.2, add new dependencies & fix build

pkgs/development/python-modules/acebinf/default.nix

@@ -0,0 +1,28 @@
+{ stdenv
+, buildPythonPackage
+, fetchPypi
+, pyvcf
+}:
+
+buildPythonPackage rec {
+  pname = "ACEBinf";
+  version = "1.0.2";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1168pny671l6zfm2vv1pwspnflmzi7f4v8yldjl7zlz0b9cm5zlz";
+  };
+
+  buildInputs = [ pyvcf ];
+
+  # no tests
+  doCheck = false;
+  pythonImportsCheck = [ "acebinf" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/ACEnglish/acebinf";
+    description = "Collection of simple utilities used when building bioinformatics tools";
+    license = licenses.unlicense;
+    maintainers = with maintainers; [ ris ];
+  };
+}

pkgs/development/python-modules/bwapy/default.nix

@@ -0,0 +1,42 @@
+{ stdenv
+, buildPythonPackage
+, pythonOlder
+, fetchPypi
+, bwa
+, cffi
+, zlib
+}:
+
+buildPythonPackage rec {
+  pname = "bwapy";
+  version = "0.1.4";
+  disabled = pythonOlder "3.6";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "090qwx3vl729zn3a7sksbviyg04kc71gpbm3nd8dalqp673x1npw";
+  };
+  postPatch = ''
+    # replace bundled bwa
+    rm -r bwa/*
+    cp ${bwa}/lib/*.a ${bwa}/include/*.h bwa/
+
+    substituteInPlace setup.py \
+      --replace 'setuptools>=49.2.0' 'setuptools'
+  '';
+
+  buildInputs = [ zlib bwa ];
+
+  propagatedBuildInputs = [ cffi ];
+
+  # no tests
+  doCheck = false;
+  pythonImportsCheck = [ "bwapy" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/ACEnglish/acebinf";
+    description = "Python bindings to bwa mem aligner";
+    license = licenses.mpl20;
+    maintainers = with maintainers; [ ris ];
+  };
+}

pkgs/development/python-modules/pytabix/default.nix

@@ -0,0 +1,32 @@
+{ stdenv
+, buildPythonPackage
+, isPy3k
+, fetchPypi
+, zlib
+}:
+
+buildPythonPackage rec {
+  pname = "pytabix";
+  version = "0.1";
+
+  src = fetchPypi {
+    inherit pname version;
+    sha256 = "1ldp5r4ggskji6qx4bp2qxy2vrvb3fam03ksn0gq2hdxgrlg2x07";
+  };
+
+  buildInputs = [ zlib ];
+
+  doCheck = !isPy3k;
+  preCheck = ''
+    substituteInPlace test/test.py \
+      --replace 'test_remote_file' 'dont_test_remote_file'
+  '';
+  pythonImportsCheck = [ "tabix" ];
+
+  meta = with stdenv.lib; {
+    homepage = "https://github.com/slowkow/pytabix";
+    description = "Python interface for tabix";
+    license = licenses.mit;
+    maintainers = with maintainers; [ ris ];
+  };
+}