diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
17 files changed, 107 insertions, 56 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/N3/default.nix b/nixpkgs/pkgs/applications/science/biology/N3/default.nix index 2f4aa4ce3927..e7ae8fb3cea3 100644 --- a/nixpkgs/pkgs/applications/science/biology/N3/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/N3/default.nix @@ -1,6 +1,6 @@ { lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, - libminc, EBTKS }: + libminc, ebtks }: stdenv.mkDerivation rec { pname = "N3"; @@ -13,11 +13,16 @@ stdenv.mkDerivation rec { sha256 = "06hci7gzhy8p34ggvx7gah2k9yxpwhgmq1cgw8pcd1r82g4rg6kd"; }; + postPatch = '' + substituteInPlace src/VolumeHist/DHistogram.cc \ + --replace "register " "" + ''; + nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ libminc EBTKS ]; + buildInputs = [ libminc ebtks ]; propagatedBuildInputs = with perlPackages; [ perl MNI-Perllib GetoptTabular ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${ebtks}/lib/" ]; postFixup = '' for p in $out/bin/*; do diff --git a/nixpkgs/pkgs/applications/science/biology/ants/default.nix b/nixpkgs/pkgs/applications/science/biology/ants/default.nix index cb3ec8a4f7ed..c7a1391c3007 100644 --- a/nixpkgs/pkgs/applications/science/biology/ants/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/ants/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "ANTs"; - version = "2.5.0"; + version = "2.5.1"; src = fetchFromGitHub { owner = "ANTsX"; repo = "ANTs"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-rSibcsprhMC1qsuZN8ou32QPLf8n62BiDzpnTRWRx0Q="; + hash = "sha256-q252KC6SKUN5JaQWAcsVmDprVkLXDvkYzNhC7yHJNpk="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix index 356e90555f8d..dbcecb7ac3fb 100644 --- a/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/bowtie2/default.nix @@ -12,14 +12,14 @@ stdenv.mkDerivation (finalAttrs: { pname = "bowtie2"; - version = "2.5.2"; + version = "2.5.3"; src = fetchFromGitHub { owner = "BenLangmead"; repo = "bowtie2"; rev = "refs/tags/v${finalAttrs.version}"; fetchSubmodules = true; - hash = "sha256-rWeopeYuCk9ZhJX2SFCcxZWcjXjjTiVRiwkzLQcIgd0="; + hash = "sha256-vjJRA9KFfJChxxg2wxBkwsnDw7fx5SNH3JhRXQw+7XA="; }; # because of this flag, gcc on aarch64 cannot find the Threads diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix index cbde1647db9b..605ecaadf648 100644 --- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix @@ -15,21 +15,21 @@ let cloudflareZlib = fetchFromGitHub { owner = "ningfei"; repo = "zlib"; - # HEAD revision of the gcc.amd64 branch on 2022-04-14. Reminder to update + # HEAD revision of the gcc.amd64 branch on 2023-03-28. Reminder to update # whenever bumping package version. - rev = "fda61188d1d4dcd21545c34c2a2f5cc9b0f5db4b"; - sha256 = "sha256-qySFwY0VI2BQLO2XoCZeYshXEDnHh6SmJ3MvcBUROWU="; + rev = "f49b13c3380cf9677ae9a93641ebc6f770899def"; + sha256 = "sha256-8HNFUGx2uuEb8UrGUiqkN+uVDX83YIisT2uO1Z7GCxc="; }; in stdenv.mkDerivation rec { - version = "1.0.20211006"; + version = "1.0.20230411"; pname = "dcm2niix"; src = fetchFromGitHub { owner = "rordenlab"; repo = "dcm2niix"; rev = "v${version}"; - sha256 = "sha256-fQAVOzynMdSLDfhcYWcaXkFW/mnv4zySGLVJNE7ql/c="; + sha256 = "sha256-kOVEoqrk4l6sH8iDVx1QmOYP5tCufxsWnCnn9BibZ08="; }; patches = lib.optionals withCloudflareZlib [ diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/dont-fetch-external-libs.patch b/nixpkgs/pkgs/applications/science/biology/dcm2niix/dont-fetch-external-libs.patch index 493f0fb11f46..a8f97b434fc7 100644 --- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/dont-fetch-external-libs.patch +++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/dont-fetch-external-libs.patch @@ -6,7 +6,7 @@ index 9f064eb..fe74df5 100644 -set(CLOUDFLARE_BRANCH gcc.amd64) # Cloudflare zlib branch - ExternalProject_Add(zlib -- GIT_REPOSITORY "${git_protocol}://github.com/ningfei/zlib.git" +- GIT_REPOSITORY "https://github.com/ningfei/zlib.git" - GIT_TAG "${CLOUDFLARE_BRANCH}" + URL file://@cloudflareZlib@ SOURCE_DIR cloudflare-zlib @@ -16,21 +16,10 @@ diff --git a/SuperBuild/SuperBuild.cmake b/SuperBuild/SuperBuild.cmake index 2a0a956..81354a7 100644 --- a/SuperBuild/SuperBuild.cmake +++ b/SuperBuild/SuperBuild.cmake -@@ -1,17 +1,3 @@ +@@ -1,6 +1,1 @@ -# Check if git exists -find_package(Git) -if(NOT GIT_FOUND) - message(FATAL_ERROR "Cannot find Git. Git is required for Superbuild") -endif() -- --# Use git protocol or not --option(USE_GIT_PROTOCOL "If behind a firewall turn this off to use http instead." ON) --if(USE_GIT_PROTOCOL) -- set(git_protocol "git") --else() -- set(git_protocol "https") --endif() -- - # Basic CMake build settings - if(NOT CMAKE_BUILD_TYPE) - set(CMAKE_BUILD_TYPE "Release" CACHE STRING + diff --git a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix index a199e41d50aa..a7a1f77dfe90 100644 --- a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix @@ -1,19 +1,25 @@ -{ lib, python, fetchFromGitHub }: -with python.pkgs; -buildPythonApplication rec { - pname = "deepTools"; +{ lib +, python3 +, fetchFromGitHub +}: + +python3.pkgs.buildPythonApplication rec { + pname = "deeptools"; version = "3.5.4"; + pyproject = true; src = fetchFromGitHub { owner = "deeptools"; repo = "deepTools"; rev = version; - sha256 = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI="; + hash = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI="; }; - format = "pyproject"; + nativeBuildInputs = with python3.pkgs; [ + setuptools + ]; - propagatedBuildInputs = [ + propagatedBuildInputs = with python3.pkgs; [ numpy numpydoc scipy @@ -26,7 +32,21 @@ buildPythonApplication rec { importlib-metadata ]; - nativeCheckInputs = [ pytest ]; + nativeCheckInputs = with python3.pkgs; [ + pytestCheckHook + ]; + + preCheck = '' + export PATH="$out/bin:$PATH" + ''; + + disabledTestPaths = [ + # tests trip on `len(sys.argv) == 1` + "deeptools/test/test_bigwigAverage.py" + "deeptools/test/test_bigwigCompare_and_multiBigwigSummary.py" + "deeptools/test/test_heatmapper.py" + "deeptools/test/test_multiBamSummary.py" + ]; meta = with lib; { homepage = "https://deeptools.readthedocs.io/en/develop"; diff --git a/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix b/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix index 05c445b6cd08..d7bba930abca 100644 --- a/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix @@ -8,13 +8,13 @@ python3Packages.buildPythonApplication rec { pname = "eggnog-mapper"; - version = "2.1.10"; + version = "2.1.12"; src = fetchFromGitHub { owner = "eggnogdb"; repo = pname; rev = "refs/tags/${version}"; - hash = "sha256-6R2gl2l2Cl/eva0g+kxDLBI2+5T9cFTgaGMsEfeDVU0="; + hash = "sha256-+luxXQmtGufYrA/9Ak3yKzbotOj2HM3vhIoOxE+Ty1U="; }; postPatch = '' diff --git a/nixpkgs/pkgs/applications/science/biology/hh-suite/default.nix b/nixpkgs/pkgs/applications/science/biology/hh-suite/default.nix index 2e01ace7d0f1..76c6544b3430 100644 --- a/nixpkgs/pkgs/applications/science/biology/hh-suite/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/hh-suite/default.nix @@ -1,6 +1,7 @@ { lib , stdenv , fetchFromGitHub +, fetchpatch , cmake , xxd , enableMpi ? false @@ -18,6 +19,15 @@ stdenv.mkDerivation rec { hash = "sha256-kjNqJddioCZoh/cZL3YNplweIGopWIGzCYQOnKDqZmw="; }; + patches = [ + # Should be removable as soon as this upstream PR is merged: https://github.com/soedinglab/hh-suite/pull/357 + (fetchpatch { + name = "fix-gcc13-build-issues.patch"; + url = "https://github.com/soedinglab/hh-suite/commit/cec47cba5dcd580e668b1ee507c9282fbdc8e7d7.patch"; + hash = "sha256-Msdmj9l8voPYXK0SSwUA6mEbFLBhTjjE/Kjp0VL4Kf4="; + }) + ]; + nativeBuildInputs = [ cmake xxd ]; cmakeFlags = lib.optional stdenv.hostPlatform.isx86 "-DHAVE_SSE2=1" ++ lib.optional stdenv.hostPlatform.isAarch "-DHAVE_ARM8=1" diff --git a/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/nixpkgs/pkgs/applications/science/biology/igv/default.nix index 827fdb6fa1ab..be663628a426 100644 --- a/nixpkgs/pkgs/applications/science/biology/igv/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/igv/default.nix @@ -1,11 +1,11 @@ -{ lib, stdenv, fetchzip, jdk11, wrapGAppsHook }: +{ lib, stdenv, fetchzip, jdk17, testers, wrapGAppsHook, igv }: stdenv.mkDerivation rec { pname = "igv"; - version = "2.17.0"; + version = "2.17.1"; src = fetchzip { url = "https://data.broadinstitute.org/igv/projects/downloads/${lib.versions.majorMinor version}/IGV_${version}.zip"; - sha256 = "sha256-nOwaeVIvqfHrvykfTyOdnMN6+QpsvNN14jXBQx7THsE="; + sha256 = "sha256-EXI1jVr8cJPYLLe81hzqLpP3IypHBZ0cb6z+WrDeFKQ="; }; installPhase = '' @@ -13,10 +13,10 @@ stdenv.mkDerivation rec { cp -Rv * $out/share/ sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igv.sh - sed -i 's#java#${jdk11}/bin/java#g' $out/share/igv.sh + sed -i 's#java#${jdk17}/bin/java#g' $out/share/igv.sh sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igvtools - sed -i 's#java#${jdk11}/bin/java#g' $out/share/igvtools + sed -i 's#java#${jdk17}/bin/java#g' $out/share/igvtools ln -s $out/share/igv.sh $out/bin/igv ln -s $out/share/igvtools $out/bin/igvtools @@ -26,6 +26,11 @@ stdenv.mkDerivation rec { ''; nativeBuildInputs = [ wrapGAppsHook ]; + passthru.tests.version = testers.testVersion { + package = igv; + }; + + meta = with lib; { homepage = "https://www.broadinstitute.org/igv/"; description = "A visualization tool for interactive exploration of genomic datasets"; diff --git a/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix b/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix index b4999193e177..bf24f0ce19bf 100644 --- a/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/inormalize/default.nix @@ -1,6 +1,6 @@ { lib, stdenv, fetchFromGitHub, cmake, makeWrapper, perlPackages, - libminc, EBTKS }: + libminc, ebtks }: stdenv.mkDerivation rec { pname = "inormalize"; @@ -15,11 +15,16 @@ stdenv.mkDerivation rec { patches = [ ./lgmask-interp.patch ./nu_correct_norm-interp.patch ]; + postPatch = '' + substituteInPlace inormalize.cc \ + --replace "clamp" "::clamp" + ''; + nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ libminc EBTKS ]; + buildInputs = [ libminc ebtks ]; propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${EBTKS}/lib/" ]; + cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" "-DEBTKS_DIR=${ebtks}/lib/" ]; postFixup = '' for p in $out/bin/*; do diff --git a/nixpkgs/pkgs/applications/science/biology/last/default.nix b/nixpkgs/pkgs/applications/science/biology/last/default.nix index ed8690cd9c85..96182dc835d5 100644 --- a/nixpkgs/pkgs/applications/science/biology/last/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1519"; + version = "1540"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-659YiC7NA6ottOR41jo3ayh4lwReWj46NKMhMPuebF4="; + hash = "sha256-oGGpPWWQ5EVK9n5BLQwt1Wch2Xn24B+NrKg6+VrsUMY="; }; nativeBuildInputs = [ diff --git a/nixpkgs/pkgs/applications/science/biology/obitools/obitools3.nix b/nixpkgs/pkgs/applications/science/biology/obitools/obitools3.nix index b38af2f64b54..9bf579a80c3b 100644 --- a/nixpkgs/pkgs/applications/science/biology/obitools/obitools3.nix +++ b/nixpkgs/pkgs/applications/science/biology/obitools/obitools3.nix @@ -17,8 +17,8 @@ python3Packages.buildPythonApplication rec { ''; preBuild = '' - substituteInPlace src/CMakeLists.txt --replace \$'{PYTHONLIB}' "$out/lib/${python3.libPrefix}/site-packages"; - export NIX_CFLAGS_COMPILE="-L $out/lib/${python3.libPrefix}/site-packages $NIX_CFLAGS_COMPILE" + substituteInPlace src/CMakeLists.txt --replace \$'{PYTHONLIB}' "$out/${python3.sitePackages}"; + export NIX_CFLAGS_COMPILE="-L $out/${python3.sitePackages} $NIX_CFLAGS_COMPILE" ''; dontConfigure = true; diff --git a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix index 7db1edcbe9e9..70f436a088e1 100644 --- a/nixpkgs/pkgs/applications/science/biology/samtools/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/samtools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "samtools"; - version = "1.19"; + version = "1.19.2"; src = fetchurl { url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-+ms7GOIIUbbzy1WvrzIF0C/LedrjuEn89S6PwQ/wi4M="; + hash = "sha256-cfYEmWaOTAjn10X7/yTBXMigl3q6sazV0rtBm9sGXpY="; }; # 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 7d1778867921..9682265b9342 100644 --- a/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/seqkit/default.nix @@ -5,16 +5,16 @@ buildGoModule rec { pname = "seqkit"; - version = "2.6.1"; + version = "2.7.0"; src = fetchFromGitHub { owner = "shenwei356"; repo = "seqkit"; rev = "v${version}"; - sha256 = "sha256-zdn5jyb8mQ8CXHu3bHpZ7+c6K6lwoSLnmhMspMeDzy0="; + sha256 = "sha256-tnVkFING9BH/iNOdKeCsSk4ln2fLUUpI5ASaQ7CCdrg="; }; - vendorHash = "sha256-iVsLJ7UcUVTg14yEdThb6HBx6XutG0m+S9OW4iiFPUE="; + vendorHash = "sha256-o7XGBI05BK7kOBagVV2eteJmkzLTmio41KOm46GdzDU="; meta = with lib; { description = "cross-platform and ultrafast toolkit for FASTA/Q file manipulation"; diff --git a/nixpkgs/pkgs/applications/science/biology/spades/default.nix b/nixpkgs/pkgs/applications/science/biology/spades/default.nix index 976dd65ef223..0b0491a71aae 100644 --- a/nixpkgs/pkgs/applications/science/biology/spades/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/spades/default.nix @@ -17,6 +17,11 @@ stdenv.mkDerivation rec { sourceRoot = "${pname}-${version}/src"; + env.CXXFLAGS = toString [ + # GCC 13: error: 'uint32_t' does not name a type + "-include cstdint" + ]; + meta = with lib; { description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"; license = licenses.gpl2Only; diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix index 0a18c5f40fda..3d385b54d469 100644 --- a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "stacks"; - version = "2.65"; + version = "2.66"; src = fetchurl { url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz"; - sha256 = "sha256-/9a9PWKVq5yJzEUfOF03zR1Hp3AZw9MF8xICoriV4uo="; + sha256 = "sha256-9pHmcLYMdn9xy3vhlOU42Io/4L61auoncfpZNRPUN/I="; }; buildInputs = [ zlib ]; diff --git a/nixpkgs/pkgs/applications/science/biology/whisper/default.nix b/nixpkgs/pkgs/applications/science/biology/whisper/default.nix index 4d74ea981098..4cc211547610 100644 --- a/nixpkgs/pkgs/applications/science/biology/whisper/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/whisper/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, fetchurl }: +{ lib, stdenv, fetchFromGitHub, fetchpatch, fetchurl }: stdenv.mkDerivation rec { pname = "whisper"; @@ -11,6 +11,16 @@ stdenv.mkDerivation rec { sha256 = "0wpx1w1mar2d6zq2v14vy6nn896ds1n3zshxhhrrj5d528504iyw"; }; + patches = [ + # gcc-13 compatibility fixes: + # https://github.com/refresh-bio/Whisper/pull/17 + (fetchpatch { + name = "gcc-13.patch"; + url = "https://github.com/refresh-bio/Whisper/commit/d67e110dd6899782e4687188f6b432494315b0b4.patch"; + hash = "sha256-Z8GrkUMIKO/ccEdwulQh+WUox3CEckr6NgoBSzYvfuw="; + }) + ]; + preConfigure = '' cd src @@ -18,6 +28,8 @@ stdenv.mkDerivation rec { sed -i 's/ -static / /' makefile ''; + enableParallelBuilding = true; + installPhase = '' runHook preInstall install -Dt $out/bin whisper whisper-index |