diff options
Diffstat (limited to 'pkgs/applications/science/biology')
37 files changed, 152 insertions, 184 deletions
diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index c7a1391c3007b..c4b932f6dbae8 100644 --- a/pkgs/applications/science/biology/ants/default.nix +++ b/pkgs/applications/science/biology/ants/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "ANTs"; - version = "2.5.1"; + version = "2.5.2"; src = fetchFromGitHub { owner = "ANTsX"; repo = "ANTs"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-q252KC6SKUN5JaQWAcsVmDprVkLXDvkYzNhC7yHJNpk="; + hash = "sha256-crvLxUP/uM0u1oakxcpsiULAKUo+86hGATs/kHNseaw="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/bedtools/default.nix b/pkgs/applications/science/biology/bedtools/default.nix index 76780298120ed..19df156ae17cc 100644 --- a/pkgs/applications/science/biology/bedtools/default.nix +++ b/pkgs/applications/science/biology/bedtools/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cxx} CC=${cc} install"; meta = with lib; { - description = "A powerful toolset for genome arithmetic"; + description = "Powerful toolset for genome arithmetic"; license = licenses.gpl2; homepage = "https://bedtools.readthedocs.io/en/latest/"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/bftools/default.nix b/pkgs/applications/science/biology/bftools/default.nix index a8bb739bbed85..6b8a7fd96d099 100644 --- a/pkgs/applications/science/biology/bftools/default.nix +++ b/pkgs/applications/science/biology/bftools/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { nativeBuildInputs = [ makeWrapper ]; meta = with lib; { - description = "A bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included"; + description = "Bundle of scripts for using Bio-Formats on the command line with bioformats_package.jar already included"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.gpl2; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/bowtie/default.nix b/pkgs/applications/science/biology/bowtie/default.nix index bec263a2d9315..2009788ead6a5 100644 --- a/pkgs/applications/science/biology/bowtie/default.nix +++ b/pkgs/applications/science/biology/bowtie/default.nix @@ -36,7 +36,7 @@ stdenv.mkDerivation rec { installFlags = [ "prefix=$(out)" ]; meta = with lib; { - description = "An ultrafast memory-efficient short read aligner"; + description = "Ultrafast memory-efficient short read aligner"; license = licenses.artistic2; homepage = "https://bowtie-bio.sourceforge.net"; maintainers = with maintainers; [ prusnak ]; diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix index dbcecb7ac3fba..576b46288c885 100644 --- a/pkgs/applications/science/biology/bowtie2/default.nix +++ b/pkgs/applications/science/biology/bowtie2/default.nix @@ -12,14 +12,14 @@ stdenv.mkDerivation (finalAttrs: { pname = "bowtie2"; - version = "2.5.3"; + version = "2.5.4"; src = fetchFromGitHub { owner = "BenLangmead"; repo = "bowtie2"; rev = "refs/tags/v${finalAttrs.version}"; fetchSubmodules = true; - hash = "sha256-vjJRA9KFfJChxxg2wxBkwsnDw7fx5SNH3JhRXQw+7XA="; + hash = "sha256-ZbmVOItfAgKdsMrvQIXgKiPtoQJZYfGblCGDoNPjvTU="; }; # because of this flag, gcc on aarch64 cannot find the Threads @@ -51,7 +51,7 @@ stdenv.mkDerivation (finalAttrs: { }; meta = with lib; { - description = "An ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; + description = "Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; license = licenses.gpl3Plus; homepage = "http://bowtie-bio.sf.net/bowtie2"; changelog = "https://github.com/BenLangmead/bowtie2/releases/tag/${finalAttrs.src.rev}"; diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix index 8c883e2617bfa..c70eba475d233 100644 --- a/pkgs/applications/science/biology/bwa/default.nix +++ b/pkgs/applications/science/biology/bwa/default.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation { ''; meta = with lib; { - description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome"; + description = "Software package for mapping low-divergent sequences against a large reference genome, such as the human genome"; mainProgram = "bwa"; license = licenses.gpl3Plus; homepage = "https://bio-bwa.sourceforge.net/"; diff --git a/pkgs/applications/science/biology/conglomerate/default.nix b/pkgs/applications/science/biology/conglomerate/default.nix index d9092b9eeb11b..0d140914638e7 100644 --- a/pkgs/applications/science/biology/conglomerate/default.nix +++ b/pkgs/applications/science/biology/conglomerate/default.nix @@ -1,20 +1,47 @@ -{ lib, stdenv, fetchFromGitHub, cmake, coreutils, perlPackages, bicpl, libminc, zlib, minc_tools, - makeWrapper }: +{ + lib, + stdenv, + fetchFromGitHub, + cmake, + coreutils, + perlPackages, + bicpl, + libminc, + zlib, + minc_tools, + makeWrapper, +}: stdenv.mkDerivation rec { pname = "conglomerate"; - version = "unstable-2017-09-10"; + version = "unstable-2023-01-19"; src = fetchFromGitHub { - owner = "BIC-MNI"; - repo = pname; - rev = "7343238bc6215942c7ecc885a224f24433a291b0"; - sha256 = "1mlqgmy3jc13bv7d01rjwldxq0p4ayqic85xcl222hhifi3w2prr"; + owner = "BIC-MNI"; + repo = pname; + rev = "6fb26084f2871a85044e2e4afc868982702b40ed"; + hash = "sha256-Inr4b2bxguzkcRQBURObsQQ0Rb3H/Zz6hEzNRd+IX3w="; }; - nativeBuildInputs = [ cmake makeWrapper ]; - buildInputs = [ libminc zlib bicpl ]; - propagatedBuildInputs = [ coreutils minc_tools ] ++ (with perlPackages; [ perl GetoptTabular MNI-Perllib ]); + nativeBuildInputs = [ + cmake + makeWrapper + ]; + buildInputs = [ + libminc + zlib + bicpl + ]; + propagatedBuildInputs = + [ + coreutils + minc_tools + ] + ++ (with perlPackages; [ + perl + GetoptTabular + MNI-Perllib + ]); cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" @@ -23,15 +50,20 @@ stdenv.mkDerivation rec { postFixup = '' for p in $out/bin/*; do - wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${lib.makeBinPath [ coreutils minc_tools ]}"; + wrapProgram $p --prefix PERL5LIB : $PERL5LIB --set PATH "${ + lib.makeBinPath [ + coreutils + minc_tools + ] + }"; done ''; - meta = with lib; { + meta = { homepage = "https://github.com/BIC-MNI/conglomerate"; description = "More command-line utilities for working with MINC files"; - maintainers = with maintainers; [ bcdarwin ]; - platforms = platforms.unix; - license = licenses.hpndUc; + maintainers = with lib.maintainers; [ bcdarwin ]; + platforms = lib.platforms.unix; + license = lib.licenses.hpndUc; }; } diff --git a/pkgs/applications/science/biology/dssp/default.nix b/pkgs/applications/science/biology/dssp/default.nix index 6c7157a91764c..56eb023805a3e 100644 --- a/pkgs/applications/science/biology/dssp/default.nix +++ b/pkgs/applications/science/biology/dssp/default.nix @@ -3,39 +3,20 @@ , cmake , eigen , fetchFromGitHub -, fetchpatch , libcifpp , libmcfp , zlib }: -let - libcifpp' = libcifpp.overrideAttrs (oldAttrs: { - # dssp 4.4.3 requires specific version "5.2.0" of libcifpp - version = "5.2.0"; - src = fetchFromGitHub { - inherit (oldAttrs.src) owner repo rev; - hash = "sha256-Sj10j6HxUoUvQ66cd2B8CO7CVBRd7w9CTovxkwPDOvs="; - }; - patches = [ - (fetchpatch { - # https://github.com/PDB-REDO/libcifpp/issues/51 - name = "fix-build-on-darwin.patch"; - url = "https://github.com/PDB-REDO/libcifpp/commit/641f06a7e7c0dc54af242b373820f2398f59e7ac.patch"; - hash = "sha256-eWNfp9nA/+2J6xjZR6Tj+5OM3L5MxdfRi0nBzyaqvS0="; - }) - ]; - }); -in stdenv.mkDerivation (finalAttrs: { pname = "dssp"; - version = "4.4.5"; + version = "4.4.7"; src = fetchFromGitHub { owner = "PDB-REDO"; repo = "dssp"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-X0aMWqoMhmQVRHWKVm2S6JAOYiBuBBMzMoivMdpNx0M="; + hash = "sha256-qePoZYkzzWuK6j1NM+q6fPuWVRDEe4OkPmXc9Nbqobo="; }; nativeBuildInputs = [ @@ -44,7 +25,7 @@ stdenv.mkDerivation (finalAttrs: { buildInputs = [ eigen - libcifpp' + libcifpp libmcfp zlib ]; diff --git a/pkgs/applications/science/biology/emboss/default.nix b/pkgs/applications/science/biology/emboss/default.nix index d590a5da8a674..90fe611209f5d 100644 --- a/pkgs/applications/science/biology/emboss/default.nix +++ b/pkgs/applications/science/biology/emboss/default.nix @@ -18,7 +18,7 @@ stdenv.mkDerivation rec { ''; meta = { - description = "The European Molecular Biology Open Software Suite"; + description = "European Molecular Biology Open Software Suite"; longDescription = ''EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community, including libraries. The software automatically copes with diff --git a/pkgs/applications/science/biology/gatk/default.nix b/pkgs/applications/science/biology/gatk/default.nix index 9884e3a771111..41623bf640dda 100644 --- a/pkgs/applications/science/biology/gatk/default.nix +++ b/pkgs/applications/science/biology/gatk/default.nix @@ -25,7 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://gatk.broadinstitute.org/hc/en-us"; - description = "A wide variety of tools with a primary focus on variant discovery and genotyping." ; + description = "Wide variety of tools with a primary focus on variant discovery and genotyping." ; license = licenses.asl20; sourceProvenance = with lib.sourceTypes; [ binaryBytecode ] ; maintainers = with maintainers; [ apraga ]; diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 219792326b685..0c74b65c98a26 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -33,7 +33,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://www.broadinstitute.org/igv/"; - description = "A visualization tool for interactive exploration of genomic datasets"; + description = "Visualization tool for interactive exploration of genomic datasets"; license = licenses.mit; platforms = platforms.unix; maintainers = [ maintainers.mimame ]; diff --git a/pkgs/applications/science/biology/iqtree/default.nix b/pkgs/applications/science/biology/iqtree/default.nix index d8e90789f4d5f..4dfbaa25b36a4 100644 --- a/pkgs/applications/science/biology/iqtree/default.nix +++ b/pkgs/applications/science/biology/iqtree/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation rec { pname = "iqtree"; - version = "2.3.2"; + version = "2.3.4"; src = fetchFromGitHub { owner = "iqtree"; repo = "iqtree2"; rev = "v${version}"; - hash = "sha256-hAJs48PhIyZSKSRZjQJKQwoJlt6DPRQwaDsuZ00VZII="; + hash = "sha256-dnUFllqcABB3JDYoCwPGtIYD/h5lzX2XKOroDpijPpU="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/biology/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index 46a8c85d3a066..395e5b5dcd9ab 100644 --- a/pkgs/applications/science/biology/jbrowse/default.nix +++ b/pkgs/applications/science/biology/jbrowse/default.nix @@ -2,11 +2,11 @@ let pname = "jbrowse"; - version = "2.5.0"; + version = "2.11.2"; src = fetchurl { url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage"; - sha256 = "sha256-YLsyA+RVoFvjE4MfAtglJYdUgic487SxwdUhvolzBPc="; + sha256 = "sha256-7kZsK3vYgxubgtoIG1dByHgEBOlh9GUq+i3u/1eo0/o="; }; appimageContents = appimageTools.extractType2 { @@ -28,7 +28,7 @@ appimageTools.wrapType2 { ''; meta = with lib; { - description = "The next-generation genome browser"; + description = "Next-generation genome browser"; mainProgram = "jbrowse-desktop"; homepage = "https://jbrowse.org/jb2/"; license = licenses.asl20; diff --git a/pkgs/applications/science/biology/kalign/default.nix b/pkgs/applications/science/biology/kalign/default.nix index f26b679f799db..55df8d875bbd5 100644 --- a/pkgs/applications/science/biology/kalign/default.nix +++ b/pkgs/applications/science/biology/kalign/default.nix @@ -36,7 +36,7 @@ stdenv.mkDerivation (finalAttrs: { doCheck = true; meta = { - description = "A fast multiple sequence alignment program"; + description = "Fast multiple sequence alignment program"; mainProgram = "kalign"; homepage = "https://github.com/TimoLassmann/kalign"; changelog = "https://github.com/TimoLassmann/kalign/releases/tag/${finalAttrs.src.rev}"; diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix index b6e4661ccfd61..f30a6725bb474 100644 --- a/pkgs/applications/science/biology/kent/default.nix +++ b/pkgs/applications/science/biology/kent/default.nix @@ -13,13 +13,13 @@ }: stdenv.mkDerivation rec { pname = "kent"; - version = "446"; + version = "467"; src = fetchFromGitHub { owner = "ucscGenomeBrowser"; repo = pname; rev = "v${version}_base"; - hash = "sha256-d8gcoyMwINdHoD6xaNKt4rCKrKir99+i4KIzJ2YnxRw="; + hash = "sha256-Y8iHSo70nsPZwVy8ZiiqjU3mGrPOyPQkW0VpLS+ulGE="; }; buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 85fb1ca80ac65..7cfdb674c6e49 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1543"; + version = "1548"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-APHPv7Q64JITfHsvjCThZ6hvGHerk6wjOm32KdTv4k8="; + hash = "sha256-6mLPnyEAuRvCeV8pv3avsm6CKDrBPgX8xSxGO2kvTrM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/macs2/default.nix b/pkgs/applications/science/biology/macs2/default.nix index 26ec138048f7e..153f85535f943 100644 --- a/pkgs/applications/science/biology/macs2/default.nix +++ b/pkgs/applications/science/biology/macs2/default.nix @@ -1,9 +1,11 @@ -{ lib, python3, fetchpatch, fetchPypi }: +{ lib, python311, fetchpatch, fetchPypi }: -python3.pkgs.buildPythonPackage rec { +# pin python311 because macs2 does not support python 3.12 +# https://github.com/macs3-project/MACS/issues/598#issuecomment-1812622572 +python311.pkgs.buildPythonPackage rec { pname = "macs2"; version = "2.2.9.1"; - format = "pyproject"; + pyproject = true; src = fetchPypi { pname = lib.toUpper pname; @@ -20,20 +22,19 @@ python3.pkgs.buildPythonPackage rec { }) ]; - nativeBuildInputs = with python3.pkgs; [ + build-system = with python311.pkgs; [ cython_0 numpy setuptools - wheel ]; - propagatedBuildInputs = with python3.pkgs; [ + dependencies = with python311.pkgs; [ numpy ]; __darwinAllowLocalNetworking = true; - nativeCheckInputs = with python3.pkgs; [ + nativeCheckInputs = with python311.pkgs; [ unittestCheckHook ]; diff --git a/pkgs/applications/science/biology/megahit/default.nix b/pkgs/applications/science/biology/megahit/default.nix index 5fa9420bc87cb..185f763c2fb8c 100644 --- a/pkgs/applications/science/biology/megahit/default.nix +++ b/pkgs/applications/science/biology/megahit/default.nix @@ -28,7 +28,7 @@ stdenv.mkDerivation rec { "-DSTATIC_BUILD=ON" ]; meta = with lib; { - description = "An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"; + description = "Ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph"; license = licenses.gpl3; homepage = "https://github.com/voutcn/megahit"; maintainers = with maintainers; [ luispedro ]; diff --git a/pkgs/applications/science/biology/messer-slim/default.nix b/pkgs/applications/science/biology/messer-slim/default.nix index d463b4fe53665..3812e9980cdfe 100644 --- a/pkgs/applications/science/biology/messer-slim/default.nix +++ b/pkgs/applications/science/biology/messer-slim/default.nix @@ -1,14 +1,14 @@ { lib, stdenv, fetchFromGitHub, cmake, gcc, gcc-unwrapped }: stdenv.mkDerivation rec { - version = "4.2.1"; + version = "4.2.2"; pname = "messer-slim"; src = fetchFromGitHub { owner = "MesserLab"; repo = "SLiM"; rev = "v${version}"; - sha256 = "sha256-ba5I/bsDNAhDb1Kq0lWTC6YgpZ1PpeHPmB/vXx/JRK0="; + sha256 = "sha256-TlB7Hj4pVN4p4VanACWjQBeTxP9/DvRvdCdgelrXx60="; }; nativeBuildInputs = [ cmake gcc gcc-unwrapped ]; @@ -17,7 +17,7 @@ stdenv.mkDerivation rec { "-DCMAKE_RANLIB=${gcc-unwrapped}/bin/gcc-ranlib" ]; meta = { - description = "An evolutionary simulation framework"; + description = "Evolutionary simulation framework"; homepage = "https://messerlab.org/slim/"; license = with lib.licenses; [ gpl3 ]; maintainers = with lib.maintainers; [ bzizou ]; diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix index 31e4eb2fcb42b..7820f177bfb7b 100644 --- a/pkgs/applications/science/biology/migrate/default.nix +++ b/pkgs/applications/science/biology/migrate/default.nix @@ -1,18 +1,31 @@ -{ stdenv, lib, gccStdenv, fetchurl, zlib, mpi }: +{ + stdenv, + lib, + fetchurl, + zlib, + mpi, +}: -gccStdenv.mkDerivation rec { - version = "3.7.2"; +stdenv.mkDerivation (finalAttrs: { + version = "5.0.6"; pname = "migrate"; src = fetchurl { - url = "https://peterbeerli.com/migrate-html5/download_version3/${pname}-${version}.src.tar.gz"; - sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v"; + url = "https://peterbeerli.com/migrate-html5/download_version4/${finalAttrs.pname}-${finalAttrs.version}.src.tar.gz"; + hash = "sha256-twkoR9L6VPUye12OC0B5w0PxcxyKain6RkhCswLEdwg="; }; - buildInputs = [ zlib mpi ]; - setSourceRoot = "sourceRoot=$(echo */src)"; - buildFlags = [ "thread" "mpis" ]; - preInstall = "mkdir -p $out/man/man1"; + sourceRoot = "migrate-${finalAttrs.version}/src"; + + buildInputs = [ + zlib + mpi + ]; + + buildFlags = [ + "thread" + "mpis" + ]; meta = with lib; { broken = stdenv.isDarwin; @@ -21,5 +34,6 @@ gccStdenv.mkDerivation rec { license = licenses.mit; maintainers = [ maintainers.bzizou ]; platforms = platforms.unix; + mainProgram = "migrate-n"; }; -} +}) diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index 923d72f7fb387..5597b5504678d 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A versatile pairwise aligner for genomic and spliced nucleotide sequences"; + description = "Versatile pairwise aligner for genomic and spliced nucleotide sequences"; mainProgram = "minimap2"; homepage = "https://lh3.github.io/minimap2"; license = licenses.mit; diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index 6e5e4feb16fc6..ef79fb11a824d 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -1,6 +1,6 @@ { lib , stdenv -, fetchurl +, fetchFromGitHub , readline , xorg , mpi @@ -17,11 +17,13 @@ , useCore ? false , useRx3d ? false }: - - -stdenv.mkDerivation rec { +let + inherit (lib.lists) optionals; + inherit (lib.strings) cmakeBool; +in +stdenv.mkDerivation (finalAttrs: { pname = "neuron"; - version = "8.2.3"; + version = "8.2.4"; # format is for pythonModule conversion format = "other"; @@ -31,10 +33,10 @@ stdenv.mkDerivation rec { bison flex git - ] ++ lib.optionals useCore [ perl gsl ] - ++ lib.optionals stdenv.isDarwin [ xcbuild ]; + ] ++ optionals useCore [ perl gsl ] + ++ optionals stdenv.isDarwin [ xcbuild ]; - buildInputs = lib.optionals useIv [ + buildInputs = optionals useIv [ xorg.libX11.dev xorg.libXcomposite.dev xorg.libXext.dev @@ -47,28 +49,29 @@ stdenv.mkDerivation rec { python3.pkgs.setuptools python3.pkgs.scikit-build python3.pkgs.matplotlib - ] ++ lib.optionals useMpi [ + ] ++ optionals useMpi [ mpi - ] ++ lib.optionals useMpi [ + ] ++ optionals useMpi [ python3.pkgs.mpi4py - ] ++ lib.optionals useRx3d [ - python3.pkgs.cython + ] ++ optionals useRx3d [ + python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.4 python3.pkgs.numpy ]; - patches = [ ./neuron_darwin_rpath.patch ]; - # Patch build shells for cmake (bin, src, cmake) and submodules (external) postPatch = '' patchShebangs ./bin ./src ./external ./cmake - sed -e 's#DESTDIR =#DESTDIR = '"$out"'#' -i external/coreneuron/extra/nrnivmodl_core_makefile.in + substituteInPlace external/coreneuron/extra/nrnivmodl_core_makefile.in \ + --replace-fail \ + "DESTDIR =" \ + "DESTDIR = $out" ''; cmakeFlags = [ - "-DNRN_ENABLE_INTERVIEWS=${if useIv then "ON" else "OFF"}" - "-DNRN_ENABLE_MPI=${if useMpi then "ON" else "OFF"}" - "-DNRN_ENABLE_CORENEURON=${if useCore then "ON" else "OFF"}" - "-DNRN_ENABLE_RX3D=${if useRx3d then "ON" else "OFF"}" + (cmakeBool "NRN_ENABLE_INTERVIEWS" useIv) + (cmakeBool "NRN_ENABLE_MPI" useMpi) + (cmakeBool "NRN_ENABLE_CORENEURON" useCore) + (cmakeBool "NRN_ENABLE_RX3D" useRx3d) ]; postInstall = '' @@ -81,9 +84,12 @@ stdenv.mkDerivation rec { done ''; - src = fetchurl { - url = "https://github.com/neuronsimulator/nrn/releases/download/${version}/full-src-package-${version}.tar.gz"; - sha256 = "sha256-k8+71BRfh+a73sZho6v0QFRxVmrfx6jqrgaqammdtDI="; + src = fetchFromGitHub { + owner = "neuronsimulator"; + repo = "nrn"; + rev = finalAttrs.version; + fetchSubmodules = true; + hash = "sha256-KsULc+LHoWmrkGYebpoUot6DhStKidbLQf5a3S+pi4s="; }; meta = with lib; { @@ -101,4 +107,4 @@ stdenv.mkDerivation rec { maintainers = with maintainers; [ adev davidcromp ]; platforms = platforms.all; }; -} +}) diff --git a/pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch b/pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch deleted file mode 100644 index 1b0fa2670782a..0000000000000 --- a/pkgs/applications/science/biology/neuron/neuron_darwin_rpath.patch +++ /dev/null @@ -1,11 +0,0 @@ ---- a/src/nrnpython/setup.py.in -+++ b/src/nrnpython/setup.py.in -@@ -124,7 +124,7 @@ libdirs = [destdir + get_escaped_path("@NRN_LIBDIR@"), - rpath_prefix_flag='-Wl,-R' - extra_link_args = [@NRN_LINK_FLAGS_COMMA_SEPARATED_STRINGS@] - @MAC_DARWIN_FALSE@extra_link_args += [rpath_prefix_flag+lib_path for lib_path in libdirs] --@MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,@loader_path/../../") -+@MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,@loader_path/../../../") - @MAC_DARWIN_TRUE@extra_link_args.append("-Wl,-rpath,%s" % ivlibdir) - - # as neuron module will be built during make, add build/lib diff --git a/pkgs/applications/science/biology/platypus/default.nix b/pkgs/applications/science/biology/platypus/default.nix index d602395b87572..56e1852213961 100644 --- a/pkgs/applications/science/biology/platypus/default.nix +++ b/pkgs/applications/science/biology/platypus/default.nix @@ -30,7 +30,7 @@ in stdenv.mkDerivation { ''; meta = with lib; { - description = "The Platypus variant caller"; + description = "Platypus variant caller"; license = licenses.gpl3; homepage = "https://github.com/andyrimmer/Platypus"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/plink-ng/default.nix b/pkgs/applications/science/biology/plink-ng/default.nix index 0e65bed4cf3e4..b91655ac8fdac 100644 --- a/pkgs/applications/science/biology/plink-ng/default.nix +++ b/pkgs/applications/science/biology/plink-ng/default.nix @@ -32,7 +32,7 @@ stdenv.mkDerivation rec { meta = { broken = (stdenv.isLinux && stdenv.isAarch64); - description = "A comprehensive update to the PLINK association analysis toolset"; + description = "Comprehensive update to the PLINK association analysis toolset"; mainProgram = "plink"; homepage = "https://www.cog-genomics.org/plink2"; license = lib.licenses.gpl3; diff --git a/pkgs/applications/science/biology/poretools/default.nix b/pkgs/applications/science/biology/poretools/default.nix deleted file mode 100644 index 47ffd507efdaf..0000000000000 --- a/pkgs/applications/science/biology/poretools/default.nix +++ /dev/null @@ -1,23 +0,0 @@ -{ lib, python2Packages, fetchFromGitHub }: - -python2Packages.buildPythonPackage rec { - pname = "poretools"; - version = "unstable-2016-07-10"; - - src = fetchFromGitHub { - repo = pname; - owner = "arq5x"; - rev = "e426b1f09e86ac259a00c261c79df91510777407"; - sha256 = "0bglj833wxpp3cq430p1d3xp085ls221js2y90w7ir2x5ay8l7am"; - }; - - propagatedBuildInputs = [ python2Packages.h5py python2Packages.matplotlib python2Packages.seaborn python2Packages.pandas ]; - - meta = { - description = "a toolkit for working with nanopore sequencing data from Oxford Nanopore"; - license = lib.licenses.mit; - homepage = "https://poretools.readthedocs.io/en/latest/"; - maintainers = [ lib.maintainers.rybern ]; - broken = true; # Build error: h5py-3.9.0 not supported for interpreter python2.7 - }; -} diff --git a/pkgs/applications/science/biology/raxml/default.nix b/pkgs/applications/science/biology/raxml/default.nix index 0cc20b0635036..94ccafd36d00c 100644 --- a/pkgs/applications/science/biology/raxml/default.nix +++ b/pkgs/applications/science/biology/raxml/default.nix @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies"; + description = "Tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies"; license = licenses.gpl3; homepage = "https://sco.h-its.org/exelixis/web/software/raxml/"; maintainers = [ maintainers.unode ]; diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix index 70f436a088e1e..7e12047e095bc 100644 --- a/pkgs/applications/science/biology/samtools/default.nix +++ b/pkgs/applications/science/biology/samtools/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchurl, fetchpatch, zlib, htslib, perl, ncurses ? null }: +{ lib, stdenv, fetchurl, zlib, htslib, perl, ncurses ? null }: stdenv.mkDerivation rec { pname = "samtools"; diff --git a/pkgs/applications/science/biology/seqkit/default.nix b/pkgs/applications/science/biology/seqkit/default.nix index 5c46e25f5d6de..0fbda84ccea72 100644 --- a/pkgs/applications/science/biology/seqkit/default.nix +++ b/pkgs/applications/science/biology/seqkit/default.nix @@ -5,13 +5,13 @@ buildGoModule rec { pname = "seqkit"; - version = "2.8.1"; + version = "2.8.2"; src = fetchFromGitHub { owner = "shenwei356"; repo = "seqkit"; rev = "v${version}"; - sha256 = "sha256-LtPf99spy2ByTnSMJ5k1mWkh+Nct3Fg4Y9mXARxuXlA="; + sha256 = "sha256-jCzd36ds9YVBpnyR3gDJSX3CCVXzC9WkQWmkcDiDWfM="; }; vendorHash = "sha256-0//kySYhNmfiwiys/Ku0/8RzKpnxO0+byD8pcIkvDY0="; diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix deleted file mode 100644 index 0b0491a71aaef..0000000000000 --- a/pkgs/applications/science/biology/spades/default.nix +++ /dev/null @@ -1,32 +0,0 @@ -{ lib, stdenv, fetchurl, zlib, bzip2, cmake, python3 }: - -stdenv.mkDerivation rec { - pname = "SPAdes"; - version = "3.15.5"; - - src = fetchurl { - url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz"; - sha256 = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o="; - }; - - nativeBuildInputs = [ cmake ]; - - buildInputs = [ zlib bzip2 python3 ]; - - doCheck = true; - - sourceRoot = "${pname}-${version}/src"; - - env.CXXFLAGS = toString [ - # GCC 13: error: 'uint32_t' does not name a type - "-include cstdint" - ]; - - meta = with lib; { - description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines"; - license = licenses.gpl2Only; - homepage = "http://cab.spbu.ru/software/spades/"; - platforms = [ "x86_64-linux" "x86_64-darwin" ]; - maintainers = [ maintainers.bzizou ]; - }; -} diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix index a36157ed5d169..62c21a23eb66a 100644 --- a/pkgs/applications/science/biology/sratoolkit/default.nix +++ b/pkgs/applications/science/biology/sratoolkit/default.nix @@ -48,8 +48,8 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://github.com/ncbi/sra-tools"; - description = "The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives."; - license = licenses.publicDomain; + description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives"; + license = licenses.ncbiPd; maintainers = with maintainers; [ thyol ]; platforms = [ "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/applications/science/biology/tandem-aligner/default.nix index 0b3f2520d82be..d44489debbb62 100644 --- a/pkgs/applications/science/biology/tandem-aligner/default.nix +++ b/pkgs/applications/science/biology/tandem-aligner/default.nix @@ -56,7 +56,7 @@ stdenv.mkDerivation (finalAttrs: { ''; meta = { - description = "A parameter-free algorithm for sequence alignment"; + description = "Parameter-free algorithm for sequence alignment"; homepage = "https://github.com/seryrzu/tandem_aligner"; changelog = "https://github.com/seryrzu/tandem_aligner/releases/tag/v${finalAttrs.version}"; license = lib.licenses.bsd3; diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix index b27a63a2135ae..b2ef121caa9a2 100644 --- a/pkgs/applications/science/biology/trimal/default.nix +++ b/pkgs/applications/science/biology/trimal/default.nix @@ -22,7 +22,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - description = "A tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment"; + description = "Tool for the automated removal of spurious sequences or poorly aligned regions from a multiple sequence alignment"; license = licenses.gpl3; platforms = platforms.linux; homepage = "http://trimal.cgenomics.org"; diff --git a/pkgs/applications/science/biology/trimmomatic/default.nix b/pkgs/applications/science/biology/trimmomatic/default.nix index db19278eaa479..111a4dda9e9df 100644 --- a/pkgs/applications/science/biology/trimmomatic/default.nix +++ b/pkgs/applications/science/biology/trimmomatic/default.nix @@ -54,7 +54,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { changelog = "https://github.com/usadellab/Trimmomatic/blob/main/versionHistory.txt"; - description = "A flexible read trimming tool for Illumina NGS data"; + description = "Flexible read trimming tool for Illumina NGS data"; longDescription = '' Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data: adapter trimming, quality trimming, diff --git a/pkgs/applications/science/biology/vcftools/default.nix b/pkgs/applications/science/biology/vcftools/default.nix index a4ec84d4d5060..644c7eb2bd37b 100644 --- a/pkgs/applications/science/biology/vcftools/default.nix +++ b/pkgs/applications/science/biology/vcftools/default.nix @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { buildInputs = [ zlib perl ]; meta = with lib; { - description = "A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project"; + description = "Set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project"; license = licenses.lgpl3; platforms = platforms.linux; homepage = "https://vcftools.github.io/index.html"; diff --git a/pkgs/applications/science/biology/whisper/default.nix b/pkgs/applications/science/biology/whisper/default.nix index 4cc2115476109..a69b39f4e0898 100644 --- a/pkgs/applications/science/biology/whisper/default.nix +++ b/pkgs/applications/science/biology/whisper/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, fetchpatch, fetchurl }: +{ lib, stdenv, fetchFromGitHub, fetchpatch }: stdenv.mkDerivation rec { pname = "whisper"; diff --git a/pkgs/applications/science/biology/xenomapper/default.nix b/pkgs/applications/science/biology/xenomapper/default.nix index 194db966915e1..98ee7c2819bec 100644 --- a/pkgs/applications/science/biology/xenomapper/default.nix +++ b/pkgs/applications/science/biology/xenomapper/default.nix @@ -15,7 +15,7 @@ python3.pkgs.buildPythonApplication rec { meta = with lib; { homepage = "https://github.com/genomematt/xenomapper"; - description = "A utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins"; + description = "Utility for post processing mapped reads that have been aligned to a primary genome and a secondary genome and binning reads into species specific, multimapping in each species, unmapped and unassigned bins"; license = licenses.gpl3; platforms = platforms.all; maintainers = [ maintainers.jbedo ]; |