diff options
Diffstat (limited to 'pkgs/applications/science/biology')
18 files changed, 33 insertions, 256 deletions
diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix index c4b932f6dbae..21dbf69407f2 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${finalAttrs.version}"; - hash = "sha256-crvLxUP/uM0u1oakxcpsiULAKUo+86hGATs/kHNseaw="; + hash = "sha256-DZzuHMC0XymFCnDn+H1pRFx9jUt+s03PaN88R4ZBRwY="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/bamtools/default.nix b/pkgs/applications/science/biology/bamtools/default.nix index 602254e2966a..820459e00003 100644 --- a/pkgs/applications/science/biology/bamtools/default.nix +++ b/pkgs/applications/science/biology/bamtools/default.nix @@ -34,7 +34,7 @@ stdenv.mkDerivation (finalAttrs: { description = "C++ API & command-line toolkit for working with BAM data"; mainProgram = "bamtools"; homepage = "https://github.com/pezmaster31/bamtools"; - changelog = "https://github.com/pezmaster31/bamtools/releases/tag/${finalAttrs.src.rev}"; + changelog = "https://github.com/pezmaster31/bamtools/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; license = licenses.mit; maintainers = with maintainers; [ natsukium ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/bowtie2/default.nix b/pkgs/applications/science/biology/bowtie2/default.nix index 576b46288c88..2a1358f2e5b7 100644 --- a/pkgs/applications/science/biology/bowtie2/default.nix +++ b/pkgs/applications/science/biology/bowtie2/default.nix @@ -54,7 +54,7 @@ stdenv.mkDerivation (finalAttrs: { description = "Ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences"; license = licenses.gpl3Plus; homepage = "http://bowtie-bio.sf.net/bowtie2"; - changelog = "https://github.com/BenLangmead/bowtie2/releases/tag/${finalAttrs.src.rev}"; + changelog = "https://github.com/BenLangmead/bowtie2/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; maintainers = with maintainers; [ rybern ]; platforms = platforms.all; mainProgram = "bowtie2"; diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index a7f30dbc075d..acf43e52764d 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -21,15 +21,15 @@ let sha256 = "sha256-8HNFUGx2uuEb8UrGUiqkN+uVDX83YIisT2uO1Z7GCxc="; }; in -stdenv.mkDerivation rec { - version = "1.0.20230411"; +stdenv.mkDerivation (finalAttrs: { + version = "1.0.20240202"; pname = "dcm2niix"; src = fetchFromGitHub { owner = "rordenlab"; repo = "dcm2niix"; - rev = "v${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/dssp/default.nix b/pkgs/applications/science/biology/dssp/default.nix index 56eb023805a3..680fc67ffcd1 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 708bd0f4305a..000000000000 --- 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 e694f6c3b89f..000000000000 --- 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/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index 90d71df72147..de3e1138970b 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 = "2.12.3"; + version = "2.14.0"; src = fetchurl { url = "https://github.com/GMOD/jbrowse-components/releases/download/v${version}/jbrowse-desktop-v${version}-linux.AppImage"; - sha256 = "sha256-REJYJzjPPsRebRKdNKGIbRICe4tw7V8PxO/q53DXo3Y="; + sha256 = "sha256-fxXOUB+glJmg4WdL+mNfkp0O4iUsl8L1EuIYpBO1gRA="; }; appimageContents = appimageTools.extractType2 { diff --git a/pkgs/applications/science/biology/kalign/default.nix b/pkgs/applications/science/biology/kalign/default.nix index 55df8d875bbd..4dc720290adc 100644 --- a/pkgs/applications/science/biology/kalign/default.nix +++ b/pkgs/applications/science/biology/kalign/default.nix @@ -39,7 +39,7 @@ stdenv.mkDerivation (finalAttrs: { description = "Fast multiple sequence alignment program"; mainProgram = "kalign"; homepage = "https://github.com/TimoLassmann/kalign"; - changelog = "https://github.com/TimoLassmann/kalign/releases/tag/${finalAttrs.src.rev}"; + changelog = "https://github.com/TimoLassmann/kalign/releases/tag/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; license = lib.licenses.gpl3Plus; maintainers = with lib.maintainers; [ natsukium ]; platforms = lib.platforms.unix; diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index 55c555e387de..5eb6d40d030c 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "kallisto"; - version = "0.50.1"; + version = "0.51.0"; src = fetchFromGitHub { repo = "kallisto"; owner = "pachterlab"; rev = "v${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 f30a6725bb47..7d73ed90856d 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${version}_base"; - hash = "sha256-Y8iHSo70nsPZwVy8ZiiqjU3mGrPOyPQkW0VpLS+ulGE="; + hash = "sha256-OM/noraW2X8WV5wqWEFiI5/JPOBmsp0fTeDdcZoXxAA="; }; buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ]; diff --git a/pkgs/applications/science/biology/last/default.nix b/pkgs/applications/science/biology/last/default.nix index 7cfdb674c6e4..9057e767c175 100644 --- a/pkgs/applications/science/biology/last/default.nix +++ b/pkgs/applications/science/biology/last/default.nix @@ -9,13 +9,13 @@ stdenv.mkDerivation rec { pname = "last"; - version = "1548"; + version = "1550"; src = fetchFromGitLab { owner = "mcfrith"; repo = "last"; rev = "refs/tags/${version}"; - hash = "sha256-6mLPnyEAuRvCeV8pv3avsm6CKDrBPgX8xSxGO2kvTrM="; + hash = "sha256-kvI3m2FIPscU/a3GEH+O3yx5TgdNHdYP6OW3/mI2roM="; }; nativeBuildInputs = [ diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix index 54f5b9bbb370..88b402712016 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 807af7ce488a..96418346eeb9 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 ef79fb11a824..e54d3c9ba7a1 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/paml/default.nix b/pkgs/applications/science/biology/paml/default.nix index c593b5ed3d34..f742e33e15cf 100644 --- a/pkgs/applications/science/biology/paml/default.nix +++ b/pkgs/applications/science/biology/paml/default.nix @@ -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/${lib.removePrefix "refs/tags/" finalAttrs.src.rev}"; platforms = lib.platforms.unix; }; }) diff --git a/pkgs/applications/science/biology/sratoolkit/default.nix b/pkgs/applications/science/biology/sratoolkit/default.nix deleted file mode 100644 index 62c21a23eb66..000000000000 --- a/pkgs/applications/science/biology/sratoolkit/default.nix +++ /dev/null @@ -1,56 +0,0 @@ -{ stdenv -, lib -, fetchurl -, autoPatchelfHook -, libidn -, zlib -, bzip2 -}: - - -let - libidn11 = libidn.overrideAttrs (old: { - pname = "libidn"; - version = "1.34"; - src = fetchurl { - url = "mirror://gnu/libidn/libidn-1.34.tar.gz"; - sha256 = "0g3fzypp0xjcgr90c5cyj57apx1cmy0c6y9lvw2qdcigbyby469p"; - }; - }); - -in - -stdenv.mkDerivation rec { - pname = "sratoolkit"; - version = "2.11.3"; - - src = fetchurl { - url = "https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/${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 {} $out/bin/{} \; - ''; - - meta = with lib; { - homepage = "https://github.com/ncbi/sra-tools"; - description = "SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives"; - license = licenses.ncbiPd; - maintainers = with maintainers; [ thyol ]; - platforms = [ "x86_64-linux" ]; - }; -} diff --git a/pkgs/applications/science/biology/tandem-aligner/default.nix b/pkgs/applications/science/biology/tandem-aligner/default.nix deleted file mode 100644 index d44489debbb6..000000000000 --- a/pkgs/applications/science/biology/tandem-aligner/default.nix +++ /dev/null @@ -1,67 +0,0 @@ -{ lib -, stdenv -, fetchFromGitHub -, fetchpatch -, cmake -, zlib -}: - -stdenv.mkDerivation (finalAttrs: { - pname = "TandemAligner"; - version = "0.1"; - - src = fetchFromGitHub { - owner = "seryrzu"; - repo = "tandem_aligner"; - rev = "v${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"; - }; -}) |