git.iko.soy/typeable/nixpkgs
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Merge pull request #100814 from unode/samtools
commit46731b888631560de0b031acc0c484d0b2677688 authorJörg Thalheim <Mic92@users.noreply.github.com> dateFri 30 Oct 2020, 16:44 (6 years ago) parent4417777459c5ec
3 files changed+18−9
compare with master
unifiedsplit
pkgs/applications/science/biology/lumpy/default.nix+6−3 pkgs/applications/science/biology/samtools/default.nix+3−3 pkgs/development/python-modules/pysam/default.nix+9−3
pkgs/applications/science/biology/lumpy/default.nix+6−3
@@ -7,13 +7,14 @@ let
77
88in stdenv.mkDerivation rec {
99 pname = "lumpy";
10− version = "0.3.0";
10+ version = "0.3.1";
1111
1212 src = fetchFromGitHub {
1313 owner = "arq5x";
1414 repo = "lumpy-sv";
15− rev = version;
16− sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18";
15+ rev = "v${version}";
16+ sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
17+ fetchSubmodules = true;
1718 };
1819
1920 nativeBuildInputs = [ which ];
@@ -26,6 +27,8 @@ in stdenv.mkDerivation rec {
2627 # Use Nix htslib over bundled version
2728 sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
2829 sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
30+ # Also make sure we use the includes from Nix's htslib
31+ sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
2932 '';
3033
3134 # Upstream's makefile doesn't have an install target
pkgs/applications/science/biology/samtools/default.nix+3−3
@@ -2,11 +2,11 @@
22
33stdenv.mkDerivation rec {
44 pname = "samtools";
5− version = "1.10";
5+ version = "1.11";
66
77 src = fetchurl {
88 url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
9− sha256 = "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv";
9+ sha256 = "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2";
1010 };
1111
1212 nativeBuildInputs = [ perl ];
@@ -29,6 +29,6 @@ stdenv.mkDerivation rec {
2929 license = licenses.mit;
3030 homepage = "http://www.htslib.org/";
3131 platforms = platforms.unix;
32− maintainers = [ maintainers.mimame ];
32+ maintainers = with maintainers; [ mimame unode ];
3333 };
3434}
pkgs/development/python-modules/pysam/default.nix+9−3
@@ -80,13 +80,19 @@ buildPythonPackage rec {
8080 --deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \
8181 --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \
8282 --deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \
83− --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
84− --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
85− --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
8683 --deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \
8784 --deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \
8885 --deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \
86+ --deselect tests/AlignmentFile_test.py::TestIO::testBAM2BAM \
87+ --deselect tests/AlignmentFile_test.py::TestIO::testBAM2CRAM \
88+ --deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
89+ --deselect tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject \
90+ --deselect tests/AlignmentFile_test.py::TestIO::testOpenFromFilename \
91+ --deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
92+ --deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
93+ --deselect tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate \
8994 --deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \
95+ --deselect tests/compile_test.py::BAMTest::testCount \
9096 tests/
9197 '';
9298