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Merge pull request #100814 from unode/samtools

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Jörg Thalheim 2020-10-30 16:44:27 +01:00 committed by GitHub
parent 44177770f3 459c5ec3b1
commit 46731b8886
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3 changed files with 18 additions and 9 deletions
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9
pkgs/applications/science/biology/lumpy/default.nix
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@ -7,13 +7,14 @@ let
in stdenv.mkDerivation rec {
pname = "lumpy";
version = "0.3.0";
version = "0.3.1";
src = fetchFromGitHub {
owner = "arq5x";
repo = "lumpy-sv";
rev = version;
sha256 = "0azhzvmh9az9jcq0xprlzdz6w16azgszv4kshb903bwbnqirmk18";
rev = "v${version}";
sha256 = "0r71sg7qch8r6p6dw995znrqdj6q49hjdylhzbib2qmv8nvglhs9";
fetchSubmodules = true;
};
nativeBuildInputs = [ which ];
@ -26,6 +27,8 @@ in stdenv.mkDerivation rec {
# Use Nix htslib over bundled version
sed -i 's/lumpy_filter: htslib/lumpy_filter:/' Makefile
sed -i 's|../../lib/htslib/libhts.a|-lhts|' src/filter/Makefile
# Also make sure we use the includes from Nix's htslib
sed -i 's|../../lib/htslib/|${htslib}|' src/filter/Makefile
'';
# Upstream's makefile doesn't have an install target

6
pkgs/applications/science/biology/samtools/default.nix
View file

@ -2,11 +2,11 @@
stdenv.mkDerivation rec {
pname = "samtools";
version = "1.10";
version = "1.11";
src = fetchurl {
url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
sha256 = "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv";
sha256 = "1dp5wknak4arnw5ghhif9mmljlfnw5bgm91wib7z0j8wdjywx0z2";
};
nativeBuildInputs = [ perl ];
@ -29,6 +29,6 @@ stdenv.mkDerivation rec {
license = licenses.mit;
homepage = "http://www.htslib.org/";
platforms = platforms.unix;
maintainers = [ maintainers.mimame ];
maintainers = with maintainers; [ mimame unode ];
};
}

12
pkgs/development/python-modules/pysam/default.nix
View file

@ -80,13 +80,19 @@ buildPythonPackage rec {
--deselect tests/AlignmentFileHeader_test.py::TestHeaderBAM::test_header_content_is_as_expected \
--deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_dictionary_access_works \
--deselect tests/AlignmentFileHeader_test.py::TestHeaderCRAM::test_header_content_is_as_expected \
--deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
--deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
--deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
--deselect tests/AlignmentFile_test.py::TestDeNovoConstruction::testBAMWholeFile \
--deselect tests/AlignmentFile_test.py::TestEmptyHeader::testEmptyHeader \
--deselect tests/AlignmentFile_test.py::TestHeaderWithProgramOptions::testHeader \
--deselect tests/AlignmentFile_test.py::TestIO::testBAM2BAM \
--deselect tests/AlignmentFile_test.py::TestIO::testBAM2CRAM \
--deselect tests/AlignmentFile_test.py::TestIO::testBAM2SAM \
--deselect tests/AlignmentFile_test.py::TestIO::testFetchFromClosedFileObject \
--deselect tests/AlignmentFile_test.py::TestIO::testOpenFromFilename \
--deselect tests/AlignmentFile_test.py::TestIO::testSAM2BAM \
--deselect tests/AlignmentFile_test.py::TestIO::testWriteUncompressedBAMFile \
--deselect tests/AlignmentFile_test.py::TestIteratorRowAllBAM::testIterate \
--deselect tests/StreamFiledescriptors_test.py::StreamTest::test_text_processing \
--deselect tests/compile_test.py::BAMTest::testCount \
tests/
'';