diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
6 files changed, 70 insertions, 19 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/bamtools/default.nix b/nixpkgs/pkgs/applications/science/biology/bamtools/default.nix new file mode 100644 index 000000000000..05373dafd381 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/bamtools/default.nix @@ -0,0 +1,41 @@ +{ lib +, stdenv +, fetchFromGitHub +, cmake +, jsoncpp +, pkg-config +, zlib +}: + +stdenv.mkDerivation (finalAttrs: { + pname = "bamtools"; + version = "2.5.2"; + + src = fetchFromGitHub { + owner = "pezmaster31"; + repo = "bamtools"; + rev = "refs/tags/v${finalAttrs.version}"; + hash = "sha256-l2DmA4P1kPneTCL9YVACE6LcQHT0F+mufPyM69VkksE="; + }; + + nativeBuildInputs = [ + cmake + pkg-config + ]; + + buildInputs = [ + jsoncpp + zlib + ]; + + doCheck = true; + + meta = with lib; { + description = "C++ API & command-line toolkit for working with BAM data"; + homepage = "https://github.com/pezmaster31/bamtools"; + changelog = "https://github.com/pezmaster31/bamtools/releases/tag/${finalAttrs.src.rev}"; + license = licenses.mit; + maintainers = with maintainers; [ natsukium ]; + platforms = platforms.unix; + }; +}) diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix index 95f8a75e662c..8ec08f22b7d1 100644 --- a/nixpkgs/pkgs/applications/science/biology/last/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1460"; + version = "1471"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-9Er15zsq9Xrw66M8QOmARC1S/O5NvmpdUvOZUGc92P0="; + hash = "sha256-HQ2C7SFfJS6TOJZUm6szhu+hMm41BnH8A7DZE5yh9fM="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/macs2/default.nix b/nixpkgs/pkgs/applications/science/biology/macs2/default.nix index 934da2e8ab61..8884d41d9064 100644 --- a/nixpkgs/pkgs/applications/science/biology/macs2/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/macs2/default.nix @@ -1,31 +1,40 @@ -{ lib, python3, fetchPypi }: +{ lib, python3, fetchpatch, fetchPypi }: python3.pkgs.buildPythonPackage rec { pname = "macs2"; - version = "2.2.8"; + version = "2.2.9.1"; format = "pyproject"; src = fetchPypi { pname = lib.toUpper pname; inherit version; - hash = "sha256-KgpDasidj4yUoeQQaQA3dg5eN5Ka1xnFRpbnTvhKmOA="; + hash = "sha256-jVa8N/uCP8Y4fXgTjOloQFxUoKjNl3ZoJwX9CYMlLRY="; }; - postPatch = '' - # prevent setup.py from installing numpy - substituteInPlace setup.py \ - --replace "subprocess.call([sys.executable, \"-m\", 'pip', 'install', f'numpy{numpy_requires}'],cwd=cwd)" "0" - ''; + patches = [ + # https://github.com/macs3-project/MACS/pull/590 + (fetchpatch { + name = "remove-pip-build-dependency.patch"; + url = "https://github.com/macs3-project/MACS/commit/cf95a930daccf9f16e5b9a9224c5a2670cf67939.patch"; + hash = "sha256-WB3Ubqk5fKtZt97QYo/sZDU/yya9MUo1NL4VsKXR+Yo="; + }) + ]; nativeBuildInputs = with python3.pkgs; [ cython + numpy setuptools + wheel + ]; + + propagatedBuildInputs = with python3.pkgs; [ + numpy ]; - propagatedBuildInputs = with python3.pkgs; [ numpy ]; + __darwinAllowLocalNetworking = true; - nativeCheckInputs = [ - python3.pkgs.unittestCheckHook + nativeCheckInputs = with python3.pkgs; [ + unittestCheckHook ]; unittestFlagsArray = [ diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix index 13094e7484e6..b36104bcf769 100644 --- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix @@ -1,4 +1,4 @@ -{lib, nimPackages, fetchFromGitHub, pcre}: +{ lib, nimPackages, fetchFromGitHub, docopt, hts, pcre }: nimPackages.buildNimPackage rec { pname = "mosdepth"; @@ -12,7 +12,8 @@ nimPackages.buildNimPackage rec { sha256 = "sha256-7uteYTCbAaXedPqk0WtHpqTfUWH/+rRW8aSlFixkEko="; }; - buildInputs = with nimPackages; [ docopt hts-nim pcre ]; + buildInputs = [ docopt hts pcre ]; + nimFlags = hts.nimFlags ++ [ "--threads:off" ]; meta = with lib; { description = "fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing"; diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix index 5e18d5ead58a..b5743df9a7ca 100644 --- a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "samtools"; - version = "1.17"; + version = "1.18"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-Ot85C2KCGf1kCPFGAqTEqpDmPhizldrXIqtRlDiipyk"; + sha256 = "sha256-1ob/piECO6YYIqKlC3DoXQsY55Nx3lrbB4KFGdP8BuE="; }; # tests require `bgzip` from the htslib package diff --git a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix index e785d6c25f3f..32f46e485098 100644 --- a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix @@ -5,13 +5,13 @@ buildGoModule rec { pname = "seqkit"; - version = "2.5.0"; + version = "2.5.1"; src = fetchFromGitHub { owner = "shenwei356"; repo = "seqkit"; rev = "v${version}"; - sha256 = "sha256-pk4HNtG2x3zZ+GEH5MNn/XPNSmx8zGWbVYPGCYIZucs="; + sha256 = "sha256-aS8aTh8Lszob9It89shhKyqxCDjFs7zxE3VhMCHYaGM="; }; vendorHash = "sha256-54kb9Na76+CgW61SnXu7EfO0InH/rjliNRcH2M/gxII="; |