diff options
Diffstat (limited to 'pkgs/applications/science/biology')
50 files changed, 225 insertions, 356 deletions
diff --git a/pkgs/applications/science/biology/EZminc/default.nix b/pkgs/applications/science/biology/EZminc/default.nix index a4bb8c62f1c42..e2e33b5c5d589 100644 --- a/pkgs/applications/science/biology/EZminc/default.nix +++ b/pkgs/applications/science/biology/EZminc/default.nix @@ -1,30 +1,60 @@ -{ lib, stdenv, fetchFromGitHub, cmake, pkg-config, libminc, bicpl, itk, fftwFloat, gsl }: +{ + lib, + stdenv, + fetchFromGitHub, + cmake, + pkg-config, + perl, + libminc, + bicpl, + itk_5_2, + fftwFloat, + gsl, +}: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "EZminc"; - version = "unstable-2019-03-12"; + version = "2.2.00-unstable-2023-10-06"; src = fetchFromGitHub { - owner = "BIC-MNI"; - repo = pname; - rev = "5e3333ee356f914d34d66d33ea8df809c7f7fa51"; - sha256 = "0wy8cppf5xpgfqvgb3mqs1cjh81n6qzkk6zxv29wvng8nar9wsy4"; + owner = "BIC-MNI"; + repo = "EZminc"; + rev = "5fdf112e837000d155891e423041d7065ea13c3f"; + hash = "sha256-0KdFIWRHnIHrau0ysGMVpg3oz01UdIvna1y2I4YEWJw="; }; - nativeBuildInputs = [ cmake pkg-config ]; - buildInputs = [ itk libminc bicpl fftwFloat gsl ]; + postPatch = '' + patchShebangs scripts/* + ''; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" - "-DEZMINC_BUILD_TOOLS=TRUE" - "-DEZMINC_BUILD_MRFSEG=TRUE" - "-DEZMINC_BUILD_DD=TRUE" ]; + nativeBuildInputs = [ + cmake + pkg-config + ]; - meta = with lib; { - homepage = "https://github.com/BIC-MNI/${pname}"; + buildInputs = [ + itk_5_2 + libminc + bicpl + fftwFloat + gsl + perl + ]; + + cmakeFlags = [ + "-DLIBMINC_DIR=${libminc}/lib/cmake" + "-DEZMINC_BUILD_TOOLS=TRUE" + "-DEZMINC_BUILD_MRFSEG=TRUE" + # "-DEZMINC_BUILD_DD=TRUE" # numerous compilation issues + ]; + + doCheck = false; # test programs/data exist but no actual test harness + + meta = { + homepage = "https://github.com/BIC-MNI/EZminc"; description = "Collection of Perl and shell scripts for processing MINC files"; - maintainers = with maintainers; [ bcdarwin ]; - platforms = platforms.unix; - license = licenses.free; - broken = true; # ITK5 compatibility issue (https://github.com/BIC-MNI/EZminc/issues/15) + maintainers = with lib.maintainers; [ bcdarwin ]; + platforms = lib.platforms.linux; # can't detect opengl on Darwin + license = lib.licenses.free; }; -} +}) diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index c4b932f6dbae8..b42eb791d27f5 100644 --- a/pkgs/applications/science/biology/ants/default.nix +++ b/pkgs/applications/science/biology/ants/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "ANTs"; - version = "2.5.2"; + version = "2.5.3"; src = fetchFromGitHub { owner = "ANTsX"; repo = "ANTs"; rev = "refs/tags/v${finalAttrs.version}"; - hash = "sha256-crvLxUP/uM0u1oakxcpsiULAKUo+86hGATs/kHNseaw="; + hash = "sha256-DZzuHMC0XymFCnDn+H1pRFx9jUt+s03PaN88R4ZBRwY="; }; nativeBuildInputs = [ @@ -27,7 +27,7 @@ stdenv.mkDerivation (finalAttrs: { buildInputs = [ itk vtk - ] ++ lib.optionals stdenv.isDarwin [ + ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ Cocoa ]; diff --git a/pkgs/applications/science/biology/bamtools/default.nix b/pkgs/applications/science/biology/bamtools/default.nix index 602254e2966ad..820459e00003b 100644 --- a/pkgs/applications/science/biology/bamtools/default.nix +++ b/pkgs/applications/science/biology/bamtools/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation (finalAttrs: { description = "C++ API & command-line toolkit for working with BAM data"; mainProgram = "bamtools"; homepage = "https://github.com/pezmaster31/bamtools"; - changelog = "https://github.com/pezmaster31/bamtools/releases/tag/${finalAttrs.src.rev}"; + changelog = "https://github.com/pezmaster31/bamtools/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; license = licenses.mit; maintainers = with maintainers; [ natsukium ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/bcftools/default.nix b/pkgs/applications/science/biology/bcftools/default.nix index cafc952dec4c7..1e44835302385 100644 --- a/pkgs/applications/science/biology/bcftools/default.nix +++ b/pkgs/applications/science/biology/bcftools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "bcftools"; - version = "1.20"; + version = "1.21"; src = fetchurl { url = "https://github.com/samtools/bcftools/releases/download/${version}/${pname}-${version}.tar.bz2"; - sha256 = "sha256-MSuDKd5RMN06N2eMcSlR5h5XcVV8cSmnCjJ6MA/ahiA="; + sha256 = "sha256-UopMwdNVU2jbdacAsio8ldqJP9GCf20wRxbf1F6k4oI="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/blast/bin.nix b/pkgs/applications/science/biology/blast/bin.nix index 48537a568e4ba..1e3975f9f5ffa 100644 --- a/pkgs/applications/science/biology/blast/bin.nix +++ b/pkgs/applications/science/biology/blast/bin.nix @@ -35,9 +35,9 @@ in stdenv.mkDerivation { inherit pname version src; - nativeBuildInputs = lib.optionals stdenv.isLinux [ autoPatchelfHook ]; + nativeBuildInputs = lib.optionals stdenv.hostPlatform.isLinux [ autoPatchelfHook ]; - buildInputs = [ python3 perl ] ++ lib.optionals stdenv.isLinux [ zlib bzip2 glib libxml2 ]; + buildInputs = [ python3 perl ] ++ lib.optionals stdenv.hostPlatform.isLinux [ zlib bzip2 glib libxml2 ]; installPhase = '' runHook preInstall diff --git a/pkgs/applications/science/biology/blast/default.nix b/pkgs/applications/science/biology/blast/default.nix index 407d38970b0f8..791d6049ad6da 100644 --- a/pkgs/applications/science/biology/blast/default.nix +++ b/pkgs/applications/science/biology/blast/default.nix @@ -81,7 +81,7 @@ stdenv.mkDerivation rec { # perl is necessary in buildInputs so that installed perl scripts get patched # correctly buildInputs = [ coreutils perl gawk zlib bzip2 cpio ] - ++ lib.optionals stdenv.isDarwin [ ApplicationServices ]; + ++ lib.optionals stdenv.hostPlatform.isDarwin [ ApplicationServices ]; hardeningDisable = [ "format" ]; postInstall = '' diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix index 576b46288c885..2a1358f2e5b77 100644 --- a/pkgs/applications/science/biology/bowtie2/default.nix +++ b/pkgs/applications/science/biology/bowtie2/default.nix @@ -54,7 +54,7 @@ stdenv.mkDerivation (finalAttrs: { 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}"; + changelog = "https://github.com/BenLangmead/bowtie2/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; maintainers = with maintainers; [ rybern ]; platforms = platforms.all; mainProgram = "bowtie2"; diff --git a/pkgs/applications/science/biology/bwa-mem2/default.nix b/pkgs/applications/science/biology/bwa-mem2/default.nix index c339baf446d2d..0a2d2c8d20529 100644 --- a/pkgs/applications/science/biology/bwa-mem2/default.nix +++ b/pkgs/applications/science/biology/bwa-mem2/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation (finalAttrs: { buildInputs = [ zlib ]; # see https://github.com/bwa-mem2/bwa-mem2/issues/93 - postPatch = lib.optionalString stdenv.isDarwin '' + postPatch = lib.optionalString stdenv.hostPlatform.isDarwin '' sed -i 's/memset_s/memset8_s/g' ext/safestringlib/include/safe_mem_lib.h sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset16_s.c sed -i 's/memset_s/memset8_s/g' ext/safestringlib/safeclib/memset32_s.c diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index d7d23dd2d46ea..1263f8194c9f2 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -31,7 +31,7 @@ stdenv.mkDerivation (finalAttrs: { env.NIX_CFLAGS_COMPILE = toString [ (lib.optionalString stdenv.cc.isGNU "-std=c++11") (lib.optionalString stdenv.cc.isClang "-Wno-error=c++11-narrowing") - (lib.optionalString (stdenv.isDarwin && stdenv.isAarch64) "-Dfinite=isfinite") + (lib.optionalString (stdenv.hostPlatform.isDarwin && stdenv.hostPlatform.isAarch64) "-Dfinite=isfinite") ]; meta = with lib; { diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index a7f30dbc075df..acf43e52764da 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -21,15 +21,15 @@ let sha256 = "sha256-8HNFUGx2uuEb8UrGUiqkN+uVDX83YIisT2uO1Z7GCxc="; }; in -stdenv.mkDerivation rec { - version = "1.0.20230411"; +stdenv.mkDerivation (finalAttrs: { + version = "1.0.20240202"; pname = "dcm2niix"; src = fetchFromGitHub { owner = "rordenlab"; repo = "dcm2niix"; - rev = "v${version}"; - sha256 = "sha256-kOVEoqrk4l6sH8iDVx1QmOYP5tCufxsWnCnn9BibZ08="; + rev = "v${finalAttrs.version}"; + sha256 = "sha256-vJUPv/6KNCsU8UjwfktHdTlsweG7+UGgAEZeESfBkD8="; }; patches = lib.optionals withCloudflareZlib [ @@ -55,15 +55,16 @@ stdenv.mkDerivation rec { "-DZLIB_IMPLEMENTATION=Cloudflare" ]; - meta = with lib; { + meta = { description = "DICOM to NIfTI converter"; mainProgram = "dcm2niix"; longDescription = '' dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. ''; homepage = "https://www.nitrc.org/projects/dcm2nii"; - license = licenses.bsd3; - maintainers = with maintainers; [ ashgillman rbreslow ]; - platforms = platforms.all; + changelog = "https://github.com/rordenlab/dcm2niix/releases/tag/v${finalAttrs.version}"; + license = lib.licenses.bsd3; + maintainers = with lib.maintainers; [ ashgillman rbreslow ]; + platforms = lib.platforms.all; }; -} +}) diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix index 34ea942b4f5c7..f122b24d465f1 100644 --- a/pkgs/applications/science/biology/delly/default.nix +++ b/pkgs/applications/science/biology/delly/default.nix @@ -13,22 +13,27 @@ stdenv.mkDerivation (finalAttrs: { pname = "delly"; - version = "1.2.6"; + version = "1.2.9"; src = fetchFromGitHub { owner = "dellytools"; repo = "delly"; rev = "v${finalAttrs.version}"; - hash = "sha256-OO5nnaIcfNAV8pc03Z8YS5kE96bFOrJXA9QTiLi7vPc="; + hash = "sha256-HeLqf/bUkZQJrW1LHl3XmecW3wS3QmjifoH34VNr3A4="; }; + postPatch = lib.optionalString stdenv.cc.isClang '' + substituteInPlace Makefile \ + --replace-fail "-std=c++17" "-std=c++14" + ''; + buildInputs = [ boost bzip2 htslib xz zlib - ] ++ lib.optional stdenv.isDarwin llvmPackages.openmp; + ] ++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp; makeFlags = [ "EBROOTHTSLIB=${htslib}" diff --git a/pkgs/applications/science/biology/dssp/default.nix b/pkgs/applications/science/biology/dssp/default.nix index 56eb023805a3e..680fc67ffcd14 100644 --- a/pkgs/applications/science/biology/dssp/default.nix +++ b/pkgs/applications/science/biology/dssp/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation (finalAttrs: { description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein"; mainProgram = "mkdssp"; homepage = "https://github.com/PDB-REDO/dssp"; - changelog = "https://github.com/PDB-REDO/libcifpp/releases/tag/${finalAttrs.src.rev}"; + changelog = "https://github.com/PDB-REDO/dssp/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; license = licenses.bsd2; maintainers = with maintainers; [ natsukium ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/febio-studio/default.nix b/pkgs/applications/science/biology/febio-studio/default.nix deleted file mode 100644 index 708bd0f4305a4..0000000000000 --- a/pkgs/applications/science/biology/febio-studio/default.nix +++ /dev/null @@ -1,62 +0,0 @@ -{ lib, stdenv, fetchFromGitHub, cmake, zlib, libglvnd, libGLU, wrapQtAppsHook -, sshSupport ? true, openssl, libssh -, tetgenSupport ? true, tetgen -, ffmpegSupport ? true, ffmpeg_4 -, dicomSupport ? false, dcmtk -, withModelRepo ? true -, withCadFeatures ? false -}: - -stdenv.mkDerivation rec { - pname = "febio-studio"; - version = "1.6.1"; - - src = fetchFromGitHub { - owner = "febiosoftware"; - repo = "FEBioStudio"; - rev = "v${version}"; - sha256 = "0r6pg49i0q9idp7pjymj7mlxd63qjvmfvg0l7fmx87y1yd2hfw4h"; - }; - - patches = [ - ./febio-studio-cmake.patch # Fix Errors that appear with certain Cmake flags - ]; - - cmakeFlags = [ - "-DQt_Ver=5" - "-DNOT_FIRST=On" - "-DOpenGL_GL_PREFERENCE=GLVND" - ] - ++ lib.optional sshSupport "-DUSE_SSH=On" - ++ lib.optional tetgenSupport "-DUSE_TETGEN=On" - ++ lib.optional ffmpegSupport "-DUSE_FFMPEG=On" - ++ lib.optional dicomSupport "-DUSE_DICOM=On" - ++ lib.optional withModelRepo "-DMODEL_REPO=On" - ++ lib.optional withCadFeatures "-DCAD_FEATURES=On" - ; - - - installPhase = '' - runHook preInstall - mkdir -p $out/ - cp -R bin $out/ - runHook postInstall - ''; - - nativeBuildInputs = [ cmake wrapQtAppsHook ]; - buildInputs = [ zlib libglvnd libGLU openssl libssh ] - ++ lib.optional sshSupport openssl - ++ lib.optional tetgenSupport tetgen - ++ lib.optional ffmpegSupport ffmpeg_4 - ++ lib.optional dicomSupport dcmtk - ; - - meta = with lib; { - description = "FEBio Suite Solver"; - mainProgram = "FEBioStudio"; - license = with licenses; [ mit ]; - homepage = "https://febio.org/"; - platforms = platforms.unix; - maintainers = with maintainers; [ Scriptkiddi ]; - }; -} diff --git a/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch b/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch deleted file mode 100644 index e694f6c3b89f2..0000000000000 --- a/pkgs/applications/science/biology/febio-studio/febio-studio-cmake.patch +++ /dev/null @@ -1,38 +0,0 @@ -diff --git a/FEBioStudio/RepositoryPanel.cpp b/FEBioStudio/RepositoryPanel.cpp -index 382db303..314cdc68 100644 ---- a/FEBioStudio/RepositoryPanel.cpp -+++ b/FEBioStudio/RepositoryPanel.cpp -@@ -1364,10 +1364,10 @@ void CRepositoryPanel::loadingPageProgress(qint64 bytesSent, qint64 bytesTotal) - - #else - --CRepositoryPanel::CRepositoryPanel(CMainWindow* pwnd, QWidget* parent){} -+CRepositoryPanel::CRepositoryPanel(CMainWindow* pwnd, QDockWidget* parent){} - CRepositoryPanel::~CRepositoryPanel(){} - void CRepositoryPanel::OpenLink(const QString& link) {} --// void CRepositoryPanel::Raise() {} -+void CRepositoryPanel::Raise() {} - void CRepositoryPanel::SetModelList(){} - void CRepositoryPanel::ShowMessage(QString message) {} - void CRepositoryPanel::ShowWelcomeMessage(QByteArray messages) {} -@@ -1396,6 +1396,7 @@ void CRepositoryPanel::on_actionSearch_triggered() {} - void CRepositoryPanel::on_actionClearSearch_triggered() {} - void CRepositoryPanel::on_actionDeleteRemote_triggered() {} - void CRepositoryPanel::on_actionModify_triggered() {} -+void CRepositoryPanel::on_actionCopyPermalink_triggered() {} - void CRepositoryPanel::on_treeWidget_itemSelectionChanged() {} - void CRepositoryPanel::on_treeWidget_customContextMenuRequested(const QPoint &pos) {} - void CRepositoryPanel::DownloadItem(CustomTreeWidgetItem *item) {} -diff --git a/FEBioStudio/WzdUpload.cpp b/FEBioStudio/WzdUpload.cpp -index 5ce74346..20062e06 100644 ---- a/FEBioStudio/WzdUpload.cpp -+++ b/FEBioStudio/WzdUpload.cpp -@@ -1183,7 +1183,7 @@ void CWzdUpload::on_saveJson_triggered() - getProjectJson(&projectInfo); - - QFile file(filedlg.selectedFiles()[0]); -- file.open(QIODeviceBase::WriteOnly); -+ file.open(QIODevice::WriteOnly); - file.write(projectInfo); - file.close(); - } diff --git a/pkgs/applications/science/biology/gatk/default.nix b/pkgs/applications/science/biology/gatk/default.nix index 41623bf640dda..50dc0613c743f 100644 --- a/pkgs/applications/science/biology/gatk/default.nix +++ b/pkgs/applications/science/biology/gatk/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "gatk"; - version = "4.5.0.0"; + version = "4.6.0.0"; src = fetchzip { url = "https://github.com/broadinstitute/gatk/releases/download/${version}/gatk-${version}.zip"; - sha256 = "sha256-c3YZsSCjZY75jooiqtc8x/xsWTvYm9labUcOydDlSRQ="; + sha256 = "sha256-AwGRkgVbG2gA4K1JG0WPr4v18JHG5YzYUKdJ2EJZX+Y="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/genmap/default.nix b/pkgs/applications/science/biology/genmap/default.nix index 235135cb60506..772975fc6450b 100644 --- a/pkgs/applications/science/biology/genmap/default.nix +++ b/pkgs/applications/science/biology/genmap/default.nix @@ -15,7 +15,7 @@ stdenv.mkDerivation rec { repo = "genmap"; rev = "genmap-v${version}"; fetchSubmodules = true; - sha256 = "sha256-7sIKBRMNzyCrZ/c2nXkknb6a5YsXe6DRE2IFhp6AviY="; + hash = "sha256-7sIKBRMNzyCrZ/c2nXkknb6a5YsXe6DRE2IFhp6AviY="; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/biology/igv/default.nix b/pkgs/applications/science/biology/igv/default.nix index 0c74b65c98a26..e2502248a50ae 100644 --- a/pkgs/applications/science/biology/igv/default.nix +++ b/pkgs/applications/science/biology/igv/default.nix @@ -13,10 +13,10 @@ stdenv.mkDerivation rec { cp -Rv * $out/share/ sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igv.sh - sed -i 's#java#${jdk17}/bin/java#g' $out/share/igv.sh + sed -i 's#\bjava\b#${jdk17}/bin/java#g' $out/share/igv.sh sed -i "s#prefix=.*#prefix=$out/share#g" $out/share/igvtools - sed -i 's#java#${jdk17}/bin/java#g' $out/share/igvtools + sed -i 's#\bjava\b#${jdk17}/bin/java#g' $out/share/igvtools ln -s $out/share/igv.sh $out/bin/igv ln -s $out/share/igvtools $out/bin/igvtools diff --git a/pkgs/applications/science/biology/iqtree/default.nix b/pkgs/applications/science/biology/iqtree/default.nix index 4dfbaa25b36a4..ce6218449a7e8 100644 --- a/pkgs/applications/science/biology/iqtree/default.nix +++ b/pkgs/applications/science/biology/iqtree/default.nix @@ -10,13 +10,13 @@ stdenv.mkDerivation rec { pname = "iqtree"; - version = "2.3.4"; + version = "2.3.6"; src = fetchFromGitHub { owner = "iqtree"; repo = "iqtree2"; rev = "v${version}"; - hash = "sha256-dnUFllqcABB3JDYoCwPGtIYD/h5lzX2XKOroDpijPpU="; + hash = "sha256-8d5zqZIevv3bnq7z7Iyo/x8i445y1RAFtRMeK8s/ieQ="; fetchSubmodules = true; }; @@ -26,7 +26,7 @@ stdenv.mkDerivation rec { boost eigen zlib - ] ++ lib.optionals stdenv.isDarwin [ + ] ++ lib.optionals stdenv.hostPlatform.isDarwin [ llvmPackages.openmp ]; diff --git a/pkgs/applications/science/biology/iv/default.nix b/pkgs/applications/science/biology/iv/default.nix index ba1b91298bb32..a4b408b14a012 100644 --- a/pkgs/applications/science/biology/iv/default.nix +++ b/pkgs/applications/science/biology/iv/default.nix @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { break fi done - '' + lib.optionalString stdenv.isLinux '' + '' + lib.optionalString stdenv.hostPlatform.isLinux '' patchelf --add-needed ${libX11}/lib/libX11.so $out/lib/libIVhines.so ''; diff --git a/pkgs/applications/science/biology/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index 395e5b5dcd9ab..88db9190465f2 100644 --- a/pkgs/applications/science/biology/jbrowse/default.nix +++ b/pkgs/applications/science/biology/jbrowse/default.nix @@ -1,12 +1,12 @@ -{ lib, fetchurl, appimageTools, wrapGAppsHook3 }: +{ lib, fetchurl, appimageTools }: let pname = "jbrowse"; - version = "2.11.2"; + version = "2.15.1"; src = fetchurl { url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage"; - sha256 = "sha256-7kZsK3vYgxubgtoIG1dByHgEBOlh9GUq+i3u/1eo0/o="; + sha256 = "sha256-/dpHUrigO0wnWay0jIkg6eG75ynrVXd7zcIAss6DhSs="; }; appimageContents = appimageTools.extractType2 { diff --git a/pkgs/applications/science/biology/kalign/default.nix b/pkgs/applications/science/biology/kalign/default.nix index 55df8d875bbd5..4dc720290adce 100644 --- a/pkgs/applications/science/biology/kalign/default.nix +++ b/pkgs/applications/science/biology/kalign/default.nix @@ -39,7 +39,7 @@ stdenv.mkDerivation (finalAttrs: { description = "Fast multiple sequence alignment program"; mainProgram = "kalign"; homepage = "https://github.com/TimoLassmann/kalign"; - changelog = "https://github.com/TimoLassmann/kalign/releases/tag/${finalAttrs.src.rev}"; + changelog = "https://github.com/TimoLassmann/kalign/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; license = lib.licenses.gpl3Plus; maintainers = with lib.maintainers; [ natsukium ]; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index 55c555e387de7..a375df35dd3ee 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "kallisto"; - version = "0.50.1"; + version = "0.51.1"; src = fetchFromGitHub { repo = "kallisto"; owner = "pachterlab"; rev = "v${version}"; - sha256 = "sha256-JJZJOl4u6FzngrrMuC2AfD5ry2LBOT8tdz2piH+9LFE="; + sha256 = "sha256-hfdeztEyHvuOnLS71oSv8sPqFe2UCX5KlANqrT/Gfx8="; }; nativeBuildInputs = [ autoconf cmake ]; diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix index 56cfa5168a486..7d73ed90856dc 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 = "466"; + version = "468"; src = fetchFromGitHub { owner = "ucscGenomeBrowser"; repo = pname; rev = "v${version}_base"; - hash = "sha256-zoDZ+8G0SHKfWmkXBqp+WSjQXtmkcTIZjrjPhUIJw1c="; + hash = "sha256-OM/noraW2X8WV5wqWEFiI5/JPOBmsp0fTeDdcZoXxAA="; }; buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 700b2cf3b4548..9057e767c1759 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1544"; + version = "1550"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-jxNudfUvSqV1QUzdvG8LWtL977oho9QuOQImmwbQiIM="; + hash = "sha256-kvI3m2FIPscU/a3GEH+O3yx5TgdNHdYP6OW3/mI2roM="; }; 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/messer-slim/default.nix b/pkgs/applications/science/biology/messer-slim/default.nix index 3812e9980cdfe..24b9a96019da6 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 = "4.2.2"; + version = "4.3"; pname = "messer-slim"; src = fetchFromGitHub { owner = "MesserLab"; repo = "SLiM"; rev = "v${version}"; - sha256 = "sha256-TlB7Hj4pVN4p4VanACWjQBeTxP9/DvRvdCdgelrXx60="; + hash = "sha256-Hgh1ianEdITRUIDKLiLW32kQlPlXKIfN4PSv3cOXTGI="; }; nativeBuildInputs = [ cmake gcc gcc-unwrapped ]; diff --git a/pkgs/applications/science/biology/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix index 7820f177bfb7b..aceb010875d74 100644 --- a/pkgs/applications/science/biology/migrate/default.nix +++ b/pkgs/applications/science/biology/migrate/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation (finalAttrs: { pname = "migrate"; src = fetchurl { - url = "https://peterbeerli.com/migrate-html5/download_version4/${finalAttrs.pname}-${finalAttrs.version}.src.tar.gz"; + url = "https://peterbeerli.com/migrate-html5/download_version4/migrate-${finalAttrs.version}.src.tar.gz"; hash = "sha256-twkoR9L6VPUye12OC0B5w0PxcxyKain6RkhCswLEdwg="; }; @@ -28,7 +28,7 @@ stdenv.mkDerivation (finalAttrs: { ]; meta = with lib; { - broken = stdenv.isDarwin; + broken = stdenv.hostPlatform.isDarwin; description = "Estimates population size, migration, population splitting parameters using genetic/genomic data"; homepage = "https://peterbeerli.com/migrate-html5/index.html"; license = licenses.mit; diff --git a/pkgs/applications/science/biology/minc-tools/default.nix b/pkgs/applications/science/biology/minc-tools/default.nix index 3dece25915b47..d4b98fce87197 100644 --- a/pkgs/applications/science/biology/minc-tools/default.nix +++ b/pkgs/applications/science/biology/minc-tools/default.nix @@ -1,24 +1,54 @@ -{ lib, stdenv, fetchFromGitHub, cmake, makeWrapper, flex, bison, perl, TextFormat, - libminc, libjpeg, nifticlib, zlib }: +{ + lib, + stdenv, + fetchFromGitHub, + cmake, + makeWrapper, + flex, + bison, + perl, + TextFormat, + libminc, + libjpeg, + nifticlib, + zlib, +}: stdenv.mkDerivation rec { - pname = "minc-tools"; - version = "unstable-2020-07-25"; + pname = "minc-tools"; + version = "2.3.06-unstable-2023-08-12"; src = fetchFromGitHub { - owner = "BIC-MNI"; - repo = pname; - rev = "fb0a68a07d281e4e099c5d54df29925240de14c1"; - sha256 = "0zcv2sdj3k6k0xjqdq8j5bxq8smm48dzai90vwsmz8znmbbm6kvw"; + owner = "BIC-MNI"; + repo = pname; + rev = "c86a767dbb63aaa05ee981306fa09f6133bde427"; + hash = "sha256-PLNcuDU0ht1PcjloDhrPzpOpE42gbhPP3rfHtP7WnM4="; }; - nativeBuildInputs = [ cmake flex bison makeWrapper ]; - buildInputs = [ libminc libjpeg nifticlib zlib ]; - propagatedBuildInputs = [ perl TextFormat ]; + nativeBuildInputs = [ + cmake + flex + bison + makeWrapper + ]; - cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/cmake" - "-DZNZ_INCLUDE_DIR=${nifticlib}/include/nifti" - "-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti" ]; + buildInputs = [ + libminc + libjpeg + nifticlib + zlib + ]; + + propagatedBuildInputs = [ + perl + TextFormat + ]; + + cmakeFlags = [ + "-DLIBMINC_DIR=${libminc}/lib/cmake" + "-DZNZ_INCLUDE_DIR=${nifticlib}/include/nifti" + "-DNIFTI_INCLUDE_DIR=${nifticlib}/include/nifti" + ]; postFixup = '' for prog in minccomplete minchistory mincpik; do @@ -31,6 +61,6 @@ stdenv.mkDerivation rec { description = "Command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; - license = licenses.free; + license = licenses.free; }; } diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index 5597b5504678d..1c523a909241a 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { buildInputs = [ zlib ]; - makeFlags = lib.optionals stdenv.isAarch64 [ "arm_neon=1" "aarch64=1" ]; + makeFlags = lib.optionals stdenv.hostPlatform.isAarch64 [ "arm_neon=1" "aarch64=1" ]; installPhase = '' mkdir -p $out/bin diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix index 54f5b9bbb3703..88b402712016b 100644 --- a/pkgs/applications/science/biology/mrbayes/default.nix +++ b/pkgs/applications/science/biology/mrbayes/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, readline }: +{ lib, stdenv, fetchFromGitHub }: stdenv.mkDerivation rec { pname = "mrbayes"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. ''; - maintainers = with maintainers; [ ]; + maintainers = [ ]; license = licenses.gpl2Plus; homepage = "https://nbisweden.github.io/MrBayes/"; platforms = platforms.linux; diff --git a/pkgs/applications/science/biology/mrtrix/default.nix b/pkgs/applications/science/biology/mrtrix/default.nix index 64eafa0f69686..e17aa3ca038c7 100644 --- a/pkgs/applications/science/biology/mrtrix/default.nix +++ b/pkgs/applications/science/biology/mrtrix/default.nix @@ -102,7 +102,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - broken = (stdenv.isLinux && stdenv.isAarch64); + broken = (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64); homepage = "https://github.com/MRtrix3/mrtrix3"; description = "Suite of tools for diffusion imaging"; maintainers = with maintainers; [ bcdarwin ]; diff --git a/pkgs/applications/science/biology/muscle/default.nix b/pkgs/applications/science/biology/muscle/default.nix index cdcf6c7b50aa8..33a56d6e26d6d 100644 --- a/pkgs/applications/science/biology/muscle/default.nix +++ b/pkgs/applications/science/biology/muscle/default.nix @@ -1,10 +1,9 @@ -{ lib, stdenv, fetchFromGitHub }: +{ lib, gccStdenv, fetchFromGitHub }: -stdenv.mkDerivation rec { - pname = "muscle"; +gccStdenv.mkDerivation rec { + pname = "muscle"; version = "5.1.0"; - src = fetchFromGitHub { owner = "rcedgar"; repo = pname; @@ -14,15 +13,26 @@ stdenv.mkDerivation rec { sourceRoot = "${src.name}/src"; - installPhase = '' - install -m755 -D Linux/muscle $out/bin/muscle - ''; + patches = [ + ./muscle-darwin-g++.patch + ]; + + installPhase = + let + target = + if gccStdenv.hostPlatform.isDarwin + then "Darwin" + else "Linux"; + in + '' + install -m755 -D ${target}/muscle $out/bin/muscle + ''; meta = with lib; { description = "Multiple sequence alignment with top benchmark scores scalable to thousands of sequences"; mainProgram = "muscle"; - license = licenses.gpl3Plus; - homepage = "https://www.drive5.com/muscle/"; + license = licenses.gpl3Plus; + homepage = "https://www.drive5.com/muscle/"; maintainers = with maintainers; [ unode thyol ]; }; } diff --git a/pkgs/applications/science/biology/muscle/muscle-darwin-g++.patch b/pkgs/applications/science/biology/muscle/muscle-darwin-g++.patch new file mode 100644 index 0000000000000..41e5fc7ae476c --- /dev/null +++ b/pkgs/applications/science/biology/muscle/muscle-darwin-g++.patch @@ -0,0 +1,15 @@ + +diff --git a/Makefile b/Makefile +index df16673..be3bd0d 100644 +--- a/Makefile ++++ b/Makefile +@@ -20,9 +20,6 @@ OS := $(shell uname) + CPPFLAGS := $(CPPFLAGS) -DNDEBUG -pthread + + CXX := g++ +-ifeq ($(OS),Darwin) +- CXX := g++-11 +-endif + + CXXFLAGS := $(CXXFLAGS) -O3 -fopenmp -ffast-math + diff --git a/pkgs/applications/science/biology/nest/default.nix b/pkgs/applications/science/biology/nest/default.nix index 807af7ce488ac..9714f015f71a4 100644 --- a/pkgs/applications/science/biology/nest/default.nix +++ b/pkgs/applications/science/biology/nest/default.nix @@ -13,20 +13,19 @@ , boost , python3 , readline -, autoPatchelfHook , withPython ? false , withMpi ? false }: stdenv.mkDerivation rec { pname = "nest"; - version = "3.7"; + version = "3.8"; src = fetchFromGitHub { owner = "nest"; repo = "nest-simulator"; rev = "v${version}"; - hash = "sha256-EwhpsfRmBLJnPiH6hXQXgG9jSNoC2oqq5lZ6t038VpI="; + hash = "sha256-hysOe1ZZpCClVOGo0+UeCP7imAakXrZlnJ4V95zfiyA="; }; postPatch = '' @@ -52,7 +51,7 @@ stdenv.mkDerivation rec { python3 python3.pkgs.cython ] ++ lib.optional withMpi mpi - ++ lib.optional stdenv.isDarwin llvmPackages.openmp; + ++ lib.optional stdenv.hostPlatform.isDarwin llvmPackages.openmp; propagatedBuildInputs = with python3.pkgs; [ numpy diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index ef79fb11a824d..fe5de3c68fab5 100644 --- a/pkgs/applications/science/biology/neuron/default.nix +++ b/pkgs/applications/science/biology/neuron/default.nix @@ -23,7 +23,7 @@ let in stdenv.mkDerivation (finalAttrs: { pname = "neuron"; - version = "8.2.4"; + version = "8.2.6"; # format is for pythonModule conversion format = "other"; @@ -34,7 +34,7 @@ stdenv.mkDerivation (finalAttrs: { flex git ] ++ optionals useCore [ perl gsl ] - ++ optionals stdenv.isDarwin [ xcbuild ]; + ++ optionals stdenv.hostPlatform.isDarwin [ xcbuild ]; buildInputs = optionals useIv [ xorg.libX11.dev @@ -54,7 +54,7 @@ stdenv.mkDerivation (finalAttrs: { ] ++ optionals useMpi [ python3.pkgs.mpi4py ] ++ optionals useRx3d [ - python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.4 + python3.pkgs.cython_0 # NOTE: cython<3 is required as of 8.2.6 python3.pkgs.numpy ]; @@ -89,7 +89,7 @@ stdenv.mkDerivation (finalAttrs: { repo = "nrn"; rev = finalAttrs.version; fetchSubmodules = true; - hash = "sha256-KsULc+LHoWmrkGYebpoUot6DhStKidbLQf5a3S+pi4s="; + hash = "sha256-xASBpsF8rIzrb5G+4Qi6rvWC2wqL7nAGlSeMsBAI6WM="; }; meta = with lib; { diff --git a/pkgs/applications/science/biology/obitools/obitools3.nix b/pkgs/applications/science/biology/obitools/obitools3.nix index f415c9c39141d..53aa177307dfa 100644 --- a/pkgs/applications/science/biology/obitools/obitools3.nix +++ b/pkgs/applications/science/biology/obitools/obitools3.nix @@ -11,7 +11,7 @@ python3Packages.buildPythonApplication rec { nativeBuildInputs = [ python3Packages.cython cmake ]; - postPatch = lib.optionalString stdenv.isAarch64 '' + postPatch = lib.optionalString stdenv.hostPlatform.isAarch64 '' substituteInPlace setup.py \ --replace "'-msse2'," "" ''; diff --git a/pkgs/applications/science/biology/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix index c593b5ed3d34c..1e21d18242bd2 100644 --- a/pkgs/applications/science/biology/paml/default.nix +++ b/pkgs/applications/science/biology/paml/default.nix @@ -14,7 +14,7 @@ stdenv.mkDerivation (finalAttrs: { hash = "sha256-P/oHaLxoQzjFuvmHyRdShHv1ayruy6O/I9w8aTyya2s="; }; - env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.isDarwin "-D_POSIX_C_SOURCE"; + env.NIX_CFLAGS_COMPILE = lib.optionalString stdenv.hostPlatform.isDarwin "-D_POSIX_C_SOURCE"; preBuild = '' cd ./src/ @@ -42,7 +42,7 @@ stdenv.mkDerivation (finalAttrs: { longDescription = "PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang. ANSI C source codes are distributed for UNIX/Linux/Mac OSX, and executables are provided for MS Windows. PAML is not good for tree making. It may be used to estimate parameters and test hypotheses to study the evolutionary process, when you have reconstructed trees using other programs such as PAUP*, PHYLIP, MOLPHY, PhyML, RaxML, etc."; license = lib.licenses.gpl3Only; homepage = "http://abacus.gene.ucl.ac.uk/software/paml.html"; - changelog = "https://github.com/abacus-gene/paml/releases/tag/${finalAttrs.src.rev}"; + changelog = "https://github.com/abacus-gene/paml/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; platforms = lib.platforms.unix; }; }) diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix index 880ea77e9d245..e8786fe4b9c0e 100644 --- a/pkgs/applications/science/biology/picard-tools/default.nix +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "picard-tools"; - version = "3.1.1"; + version = "3.2.0"; src = fetchurl { url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; - sha256 = "sha256-FcefUf0KwAEEn53XubrB2991ncsCMKicf20fJG6LurQ="; + sha256 = "sha256-4lj6Lj9fphzWeZ7I4HP0mpX73OrxY9imCXGyYZuG+kE="; }; nativeBuildInputs = [ makeWrapper ]; diff --git a/pkgs/applications/science/biology/plink-ng/default.nix b/pkgs/applications/science/biology/plink-ng/default.nix index b91655ac8fdac..b66bed97a94a5 100644 --- a/pkgs/applications/science/biology/plink-ng/default.nix +++ b/pkgs/applications/science/biology/plink-ng/default.nix @@ -11,7 +11,7 @@ stdenv.mkDerivation rec { sha256 = "1zhffjbwpd50dxywccbnv1rxy9njwz73l4awc5j7i28rgj3davcq"; }; - buildInputs = [ zlib ] ++ (if stdenv.isDarwin then [ darwin.apple_sdk.frameworks.Accelerate ] else [ blas lapack ]) ; + buildInputs = [ zlib ] ++ (if stdenv.hostPlatform.isDarwin then [ darwin.apple_sdk.frameworks.Accelerate ] else [ blas lapack ]) ; preBuild = '' sed -i 's|zlib-1.2.8/zlib.h|zlib.h|g' *.c *.h @@ -31,7 +31,7 @@ stdenv.mkDerivation rec { ''; meta = { - broken = (stdenv.isLinux && stdenv.isAarch64); + broken = (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64); description = "Comprehensive update to the PLINK association analysis toolset"; mainProgram = "plink"; homepage = "https://www.cog-genomics.org/plink2"; diff --git a/pkgs/applications/science/biology/repseek/default.nix b/pkgs/applications/science/biology/repseek/default.nix index e5e0193f7911a..9b38171b34ef2 100644 --- a/pkgs/applications/science/biology/repseek/default.nix +++ b/pkgs/applications/science/biology/repseek/default.nix @@ -13,7 +13,7 @@ stdenv.mkDerivation rec { substituteInPlace Makefile \ --replace "INSTALLDIR = \$\$HOME/bin" "INSTALLDIR = $out/bin/" \ --replace "CC= gcc" "CC = $CC" - '' + lib.optionalString stdenv.isLinux '' + '' + lib.optionalString stdenv.hostPlatform.isLinux '' substituteInPlace Makefile --replace "MACHINE = MACOSX" "MACHINE = LINUX" ''; diff --git a/pkgs/applications/science/biology/sambamba/default.nix b/pkgs/applications/science/biology/sambamba/default.nix index b6635f02aacdf..e62a5bb14aae4 100644 --- a/pkgs/applications/science/biology/sambamba/default.nix +++ b/pkgs/applications/science/biology/sambamba/default.nix @@ -16,7 +16,7 @@ stdenv.mkDerivation rec { owner = "biod"; repo = "sambamba"; rev = "v${version}"; - sha256 = "sha256-3O9bHGpMuCgdR2Wm7Dv1VUjMT1QTn8K1hdwgjvwhFDw="; + hash = "sha256-3O9bHGpMuCgdR2Wm7Dv1VUjMT1QTn8K1hdwgjvwhFDw="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/biology/sortmerna/default.nix b/pkgs/applications/science/biology/sortmerna/default.nix index c19556318843b..b6291ea852975 100644 --- a/pkgs/applications/science/biology/sortmerna/default.nix +++ b/pkgs/applications/science/biology/sortmerna/default.nix @@ -56,6 +56,6 @@ stdenv.mkDerivation rec { platforms = platforms.x86_64; homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/"; maintainers = with maintainers; [ luispedro ]; - broken = stdenv.isDarwin; + broken = stdenv.hostPlatform.isDarwin; }; } diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix deleted file mode 100644 index 62c21a23eb66a..0000000000000 --- a/pkgs/applications/science/biology/sratoolkit/default.nix +++ /dev/null @@ -1,56 +0,0 @@ -{ stdenv -, lib -, fetchurl -, autoPatchelfHook -, libidn -, zlib -, bzip2 -}: - - -let - libidn11 = libidn.overrideAttrs (old: { - pname = "libidn"; - version = "1.34"; - src = fetchurl { - url = "mirror://gnu/libidn/libidn-1.34.tar.gz"; - sha256 = "0g3fzypp0xjcgr90c5cyj57apx1cmy0c6y9lvw2qdcigbyby469p"; - }; - }); - -in - -stdenv.mkDerivation rec { - pname = "sratoolkit"; - version = "2.11.3"; - - src = fetchurl { - url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${version}/sratoolkit.${version}-ubuntu64.tar.gz"; - sha256 = "1590lc4cplxr3lhjqci8fjncy67imn2h14qd2l87chmhjh243qvx"; - }; - - nativeBuildInputs = [ - autoPatchelfHook - ]; - - buildInputs = [ - libidn11 - zlib - bzip2 - stdenv.cc.cc.lib - ]; - - sourceRoot = "sratoolkit.${version}-ubuntu64/bin"; - - installPhase = '' - find -L . -executable -type f -! -name "*remote-fuser*" -exec install -m755 -D {} $out/bin/{} \; - ''; - - meta = with lib; { - homepage = "https://github.com/ncbi/sra-tools"; - description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives"; - license = licenses.ncbiPd; - maintainers = with maintainers; [ thyol ]; - platforms = [ "x86_64-linux" ]; - }; -} diff --git a/pkgs/applications/science/biology/subread/default.nix b/pkgs/applications/science/biology/subread/default.nix index 62ea61af91926..d2ee518883b54 100644 --- a/pkgs/applications/science/biology/subread/default.nix +++ b/pkgs/applications/science/biology/subread/default.nix @@ -19,7 +19,7 @@ stdenv.mkDerivation rec { configurePhase = '' cd src - cp Makefile.${if stdenv.isLinux then "Linux" else "MacOS"} Makefile + cp Makefile.${if stdenv.hostPlatform.isLinux then "Linux" else "MacOS"} Makefile ''; makeFlags = [ "CC_EXEC=cc" ]; @@ -30,7 +30,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - broken = stdenv.isDarwin; + broken = stdenv.hostPlatform.isDarwin; description = "High-performance read alignment, quantification and mutation discovery"; license = licenses.gpl3; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix index fec5a5a3b92dc..cdb6c4f9c8aa4 100644 --- a/pkgs/applications/science/biology/svaba/default.nix +++ b/pkgs/applications/science/biology/svaba/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - broken = (stdenv.isLinux && stdenv.isAarch64); + broken = (stdenv.hostPlatform.isLinux && stdenv.hostPlatform.isAarch64); description = "Structural variant and INDEL caller for DNA sequencing data, using genome-wide local assembly"; mainProgram = "svaba"; license = licenses.gpl3; diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/applications/science/biology/tandem-aligner/default.nix deleted file mode 100644 index d44489debbb62..0000000000000 --- a/pkgs/applications/science/biology/tandem-aligner/default.nix +++ /dev/null @@ -1,67 +0,0 @@ -{ lib -, stdenv -, fetchFromGitHub -, fetchpatch -, cmake -, zlib -}: - -stdenv.mkDerivation (finalAttrs: { - pname = "TandemAligner"; - version = "0.1"; - - src = fetchFromGitHub { - owner = "seryrzu"; - repo = "tandem_aligner"; - rev = "v${finalAttrs.version}"; - hash = "sha256-iMDj1HZ8LzmZckuAM3lbG3eSJSd/5JGVA6SBs7+AgX8="; - }; - - patches = [ - (fetchpatch { - # https://github.com/seryrzu/tandem_aligner/pull/4 - url = "https://github.com/seryrzu/tandem_aligner/commit/8b516c94f90aaa9cb84278aa811285d4204b03a9.patch"; - hash = "sha256-kD46SykXklG/avK0+sc61YKFw9Bes8ZgFAjVXmcpN8k="; - stripLen = 1; - }) - ]; - - sourceRoot = "${finalAttrs.src.name}/tandem_aligner"; - - nativeBuildInputs = [ cmake ]; - - buildInputs = [ zlib ]; - - installPhase = '' - runHook preInstall - mkdir -p $out/bin - cp src/projects/tandem_aligner/tandem_aligner $out/bin - runHook postInstall - ''; - - doCheck = true; - - # adapted from target test_launch in Makefile - checkPhase = '' - runHook preCheck - mkdir -p $TMPDIR/test_launch - src/projects/tandem_aligner/tandem_aligner \ - --first $src/tandem_aligner/test_dataset/first.fasta \ - --second $src/tandem_aligner/test_dataset/second.fasta \ - -o $TMPDIR/test_launch \ - --debug - grep -q "Thank you for using TandemAligner!" $TMPDIR/test_launch/tandem_aligner.log - diff $TMPDIR/test_launch/cigar.txt $src/tandem_aligner/test_dataset/true_cigar.txt - runHook postCheck - ''; - - meta = { - description = "Parameter-free algorithm for sequence alignment"; - homepage = "https://github.com/seryrzu/tandem_aligner"; - changelog = "https://github.com/seryrzu/tandem_aligner/releases/tag/v${finalAttrs.version}"; - license = lib.licenses.bsd3; - maintainers = with lib.maintainers; [ amesgen ]; - platforms = lib.platforms.linux; - mainProgram = "tandem_aligner"; - }; -}) diff --git a/pkgs/applications/science/biology/trimal/default.nix b/pkgs/applications/science/biology/trimal/default.nix index b2ef121caa9a2..f822fe50b1648 100644 --- a/pkgs/applications/science/biology/trimal/default.nix +++ b/pkgs/applications/science/biology/trimal/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "trimal"; - version = "1.4.1"; + version = "1.5.0"; src = fetchFromGitHub { repo = pname; owner = "scapella"; rev = "v${version}"; - sha256 = "0isc7s3514di4z953xq53ncjkbi650sh4q9yyw5aag1n9hqnh7k0"; + sha256 = "sha256-6GXirih7nY0eD2XS8aplLcYf53EeLuae+ewdUgBiKQQ="; }; postUnpack = '' diff --git a/pkgs/applications/science/biology/truvari/default.nix b/pkgs/applications/science/biology/truvari/default.nix index 946f4be606326..3c523b21fc641 100644 --- a/pkgs/applications/science/biology/truvari/default.nix +++ b/pkgs/applications/science/biology/truvari/default.nix @@ -15,14 +15,14 @@ let }; in python3Packages.buildPythonApplication rec { pname = "truvari"; - version = "4.1.0"; + version = "4.2.2"; pyproject = true; src = fetchFromGitHub { owner = "ACEnglish"; repo = "truvari"; rev = "v${version}"; - hash = "sha256-HFVAv1TTL/nMjr62tQKhMdwh25P/y4nBGzSbxoJxMmo="; + hash = "sha256-SFBVatcVavBfQtFbBcXifBX3YnKsxJS669vCcyjsBA4="; }; postPatch = '' @@ -31,11 +31,11 @@ in python3Packages.buildPythonApplication rec { patchShebangs repo_utils/test_files ''; - nativeBuildInputs = [ + build-system = [ python3Packages.setuptools ]; - propagatedBuildInputs = with python3Packages; [ + dependencies = with python3Packages; [ pywfa rich edlib @@ -46,6 +46,7 @@ in python3Packages.buildPythonApplication rec { pytabix bwapy pandas + pyabpoa ]; makeWrapperArgs = [ diff --git a/pkgs/applications/science/biology/veryfasttree/default.nix b/pkgs/applications/science/biology/veryfasttree/default.nix index 6c054fecd7428..27c34f67d952a 100644 --- a/pkgs/applications/science/biology/veryfasttree/default.nix +++ b/pkgs/applications/science/biology/veryfasttree/default.nix @@ -7,13 +7,13 @@ stdenv.mkDerivation (finalAttrs: { pname = "veryfasttree"; - version = "4.0.3"; + version = "4.0.4"; src = fetchFromGitHub { owner = "citiususc"; repo = "veryfasttree"; rev = "v${finalAttrs.version}"; - hash = "sha256-Sp331VJRaYv/BTwFj3HwUcUsWjYf6YEXWjYdOzDhBBA="; + hash = "sha256-S4FW91VEdTPOIwRamz62arLSN9inxoKXpKsen2ISXMo="; }; nativeBuildInputs = [ cmake ]; diff --git a/pkgs/applications/science/biology/whisper/default.nix b/pkgs/applications/science/biology/whisper/default.nix index a69b39f4e0898..6c8bb21df6a52 100644 --- a/pkgs/applications/science/biology/whisper/default.nix +++ b/pkgs/applications/science/biology/whisper/default.nix @@ -37,7 +37,7 @@ stdenv.mkDerivation rec { ''; meta = with lib; { - broken = stdenv.isDarwin; + broken = stdenv.hostPlatform.isDarwin; description = "Short read sequence mapper"; license = licenses.gpl3; homepage = "https://github.com/refresh-bio/whisper"; |