diff options
Diffstat (limited to 'pkgs/applications/science/biology')
20 files changed, 48 insertions, 269 deletions
diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index c4b932f6dbae8..21dbf69407f21 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${finalAttrs.version}"; - hash = "sha256-crvLxUP/uM0u1oakxcpsiULAKUo+86hGATs/kHNseaw="; + hash = "sha256-DZzuHMC0XymFCnDn+H1pRFx9jUt+s03PaN88R4ZBRwY="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index a7f30dbc075df..acf43e52764da 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -21,15 +21,15 @@ let sha256 = "sha256-8HNFUGx2uuEb8UrGUiqkN+uVDX83YIisT2uO1Z7GCxc="; }; in -stdenv.mkDerivation rec { - version = "1.0.20230411"; +stdenv.mkDerivation (finalAttrs: { + version = "1.0.20240202"; pname = "dcm2niix"; src = fetchFromGitHub { owner = "rordenlab"; repo = "dcm2niix"; - rev = "v${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/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/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/iqtree/default.nix b/pkgs/applications/science/biology/iqtree/default.nix index 4dfbaa25b36a4..60827b8e3a685 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 = "2.3.5"; src = fetchFromGitHub { owner = "iqtree"; repo = "iqtree2"; rev = "v${version}"; - hash = "sha256-dnUFllqcABB3JDYoCwPGtIYD/h5lzX2XKOroDpijPpU="; + hash = "sha256-ld+9vPJRVHMEe5/igqRr6RkISY2ipfGkJFHDOSZuAmg="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/biology/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index 3a7e009cc1561..ce39ca8f425ac 100644 --- a/pkgs/applications/science/biology/jbrowse/default.nix +++ b/pkgs/applications/science/biology/jbrowse/default.nix @@ -1,12 +1,12 @@ -{ lib, fetchurl, appimageTools, wrapGAppsHook3 }: +{ lib, fetchurl, appimageTools }: let pname = "jbrowse"; - version = "2.12.2"; + version = "2.13.1"; src = fetchurl { url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage"; - sha256 = "sha256-dnvs+niNo8VPuOk9uODezLxdghwutLuhgG5Jyxi8mW0="; + sha256 = "sha256-JxV7ZxA3/YMG6ziYOA8QiBVth9UunVGJLTy1E110y6w="; }; appimageContents = appimageTools.extractType2 { diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index 55c555e387de7..5eb6d40d030c8 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "kallisto"; - version = "0.50.1"; + version = "0.51.0"; src = fetchFromGitHub { repo = "kallisto"; owner = "pachterlab"; rev = "v${version}"; - sha256 = "sha256-JJZJOl4u6FzngrrMuC2AfD5ry2LBOT8tdz2piH+9LFE="; + sha256 = "sha256-+tnuka6uzoNr5pLuE2yV97KmqdThIG0IwiO+SCYiCk8="; }; nativeBuildInputs = [ autoconf cmake ]; diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix index f30a6725bb474..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 = "467"; + version = "468"; src = fetchFromGitHub { owner = "ucscGenomeBrowser"; repo = pname; rev = "v${version}_base"; - hash = "sha256-Y8iHSo70nsPZwVy8ZiiqjU3mGrPOyPQkW0VpLS+ulGE="; + hash = "sha256-OM/noraW2X8WV5wqWEFiI5/JPOBmsp0fTeDdcZoXxAA="; }; buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 7cfdb674c6e49..9057e767c1759 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1548"; + version = "1550"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-6mLPnyEAuRvCeV8pv3avsm6CKDrBPgX8xSxGO2kvTrM="; + 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/migrate/default.nix b/pkgs/applications/science/biology/migrate/default.nix index 7820f177bfb7b..53fc807776126 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-${finalAttrs.version}.src.tar.gz"; hash = "sha256-twkoR9L6VPUye12OC0B5w0PxcxyKain6RkhCswLEdwg="; }; diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix index 54f5b9bbb3703..88b402712016b 100644 --- a/pkgs/applications/science/biology/mrbayes/default.nix +++ b/pkgs/applications/science/biology/mrbayes/default.nix @@ -1,4 +1,4 @@ -{ lib, stdenv, fetchFromGitHub, readline }: +{ lib, stdenv, fetchFromGitHub }: stdenv.mkDerivation rec { pname = "mrbayes"; @@ -23,7 +23,7 @@ stdenv.mkDerivation rec { MrBayes uses a simulation technique called Markov chain Monte Carlo (or MCMC) to approximate the posterior probabilities of trees. ''; - maintainers = with maintainers; [ ]; + maintainers = [ ]; license = licenses.gpl2Plus; homepage = "https://nbisweden.github.io/MrBayes/"; platforms = platforms.linux; diff --git a/pkgs/applications/science/biology/nest/default.nix b/pkgs/applications/science/biology/nest/default.nix index 807af7ce488ac..96418346eeb9e 100644 --- a/pkgs/applications/science/biology/nest/default.nix +++ b/pkgs/applications/science/biology/nest/default.nix @@ -13,20 +13,19 @@ , boost , python3 , readline -, autoPatchelfHook , withPython ? false , withMpi ? false }: stdenv.mkDerivation rec { pname = "nest"; - version = "3.7"; + version = "3.8"; src = fetchFromGitHub { owner = "nest"; repo = "nest-simulator"; rev = "v${version}"; - hash = "sha256-EwhpsfRmBLJnPiH6hXQXgG9jSNoC2oqq5lZ6t038VpI="; + hash = "sha256-hysOe1ZZpCClVOGo0+UeCP7imAakXrZlnJ4V95zfiyA="; }; postPatch = '' diff --git a/pkgs/applications/science/biology/neuron/default.nix b/pkgs/applications/science/biology/neuron/default.nix index ef79fb11a824d..e54d3c9ba7a12 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"; @@ -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/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${version}"; - sha256 = "sha256-3O9bHGpMuCgdR2Wm7Dv1VUjMT1QTn8K1hdwgjvwhFDw="; + hash = "sha256-3O9bHGpMuCgdR2Wm7Dv1VUjMT1QTn8K1hdwgjvwhFDw="; fetchSubmodules = true; }; diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix deleted file mode 100644 index 62c21a23eb66a..0000000000000 --- a/pkgs/applications/science/biology/sratoolkit/default.nix +++ /dev/null @@ -1,56 +0,0 @@ -{ stdenv -, lib -, fetchurl -, autoPatchelfHook -, libidn -, zlib -, bzip2 -}: - - -let - libidn11 = libidn.overrideAttrs (old: { - pname = "libidn"; - version = "1.34"; - src = fetchurl { - url = "mirror://gnu/libidn/libidn-1.34.tar.gz"; - sha256 = "0g3fzypp0xjcgr90c5cyj57apx1cmy0c6y9lvw2qdcigbyby469p"; - }; - }); - -in - -stdenv.mkDerivation rec { - pname = "sratoolkit"; - version = "2.11.3"; - - src = fetchurl { - url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${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 {} $out/bin/{} \; - ''; - - meta = with lib; { - homepage = "https://github.com/ncbi/sra-tools"; - description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives"; - license = licenses.ncbiPd; - maintainers = with maintainers; [ thyol ]; - platforms = [ "x86_64-linux" ]; - }; -} diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/applications/science/biology/tandem-aligner/default.nix deleted file mode 100644 index d44489debbb62..0000000000000 --- a/pkgs/applications/science/biology/tandem-aligner/default.nix +++ /dev/null @@ -1,67 +0,0 @@ -{ lib -, stdenv -, fetchFromGitHub -, fetchpatch -, cmake -, zlib -}: - -stdenv.mkDerivation (finalAttrs: { - pname = "TandemAligner"; - version = "0.1"; - - src = fetchFromGitHub { - owner = "seryrzu"; - repo = "tandem_aligner"; - rev = "v${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 = [ |