diff options
Diffstat (limited to 'pkgs/applications/science/biology')
48 files changed, 109 insertions, 27 deletions
diff --git a/pkgs/applications/science/biology/aragorn/default.nix b/pkgs/applications/science/biology/aragorn/default.nix index 4ee8501e8e13..3ec62ada04c9 100644 --- a/pkgs/applications/science/biology/aragorn/default.nix +++ b/pkgs/applications/science/biology/aragorn/default.nix @@ -44,6 +44,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Detects tRNA, mtRNA, and tmRNA genes in nucleotide sequences"; + mainProgram = "aragorn"; homepage = "http://www.ansikte.se/ARAGORN/"; license = licenses.gpl3Plus; maintainers = [ maintainers.bzizou ]; diff --git a/pkgs/applications/science/biology/astral/default.nix b/pkgs/applications/science/biology/astral/default.nix index 6a9513c6b817..34077949b97d 100644 --- a/pkgs/applications/science/biology/astral/default.nix +++ b/pkgs/applications/science/biology/astral/default.nix @@ -2,59 +2,78 @@ , stdenvNoCC , fetchFromGitHub , jdk8 -, makeWrapper , jre8 +, strip-nondeterminism +, makeWrapper , zip }: + let jdk = jdk8; jre = jre8; in -stdenvNoCC.mkDerivation rec { +stdenvNoCC.mkDerivation (finalAttrs: { pname = "astral"; version = "5.7.1"; src = fetchFromGitHub { owner = "smirarab"; repo = "ASTRAL"; - rev = "v${version}"; - sha256 = "043w2z6gbrisqirdid022f4b8jps1pp5syi344krv2bis1gjq5sn"; + rev = "v${finalAttrs.version}"; + hash = "sha256-VhcsX9BxiZ0nISN6Xe4N+kq0iBMCtNhyxDrm9cwXfBA="; }; - nativeBuildInputs = [ jdk makeWrapper jre zip ]; + patches = [ + # we can't use stripJavaArchivesHook here, because the build process puts a .jar file into a zip file + # this patch calls strip-nondeterminism manually + ./make-deterministic.patch + ]; + + nativeBuildInputs = [ + jdk + zip + strip-nondeterminism + makeWrapper + ]; buildPhase = '' + runHook preBuild patchShebangs ./make.sh ./make.sh + runHook postBuild ''; doCheck = true; checkPhase = '' runHook preCheck - java -jar astral.${version}.jar -i main/test_data/song_primates.424.gene.tre + java -jar astral.${finalAttrs.version}.jar -i main/test_data/song_primates.424.gene.tre runHook postCheck ''; installPhase = '' - mkdir -p $out/share/lib - mkdir -p $out/bin - mv astral.${version}.jar $out/share/ - mv lib/*.jar $out/share/lib - mv Astral.${version}.zip $out/share/ - cp -a main/test_data $out/share/ + runHook preInstall + + install -Dm644 astral.${finalAttrs.version}.jar -t $out/share + install -Dm644 lib/*.jar -t $out/share/lib + install -Dm644 Astral.${finalAttrs.version}.zip -t $out/share + cp -a main/test_data $out/share + makeWrapper ${jre}/bin/java $out/bin/astral \ - --add-flags "-jar $out/share/astral.${version}.jar" + --add-flags "-jar $out/share/astral.${finalAttrs.version}.jar" + + runHook postInstall ''; meta = with lib; { homepage = "https://github.com/smirarab/ASTRAL"; description = "Tool for estimating an unrooted species tree given a set of unrooted gene trees"; + mainProgram = "astral"; sourceProvenance = with sourceTypes; [ fromSource - binaryBytecode # source bundles dependencies as jars + binaryBytecode # source bundles dependencies as jars ]; license = licenses.asl20; - maintainers = with maintainers; [ bzizou ]; + maintainers = with maintainers; [ bzizou tomasajt ]; }; -} +}) diff --git a/pkgs/applications/science/biology/astral/make-deterministic.patch b/pkgs/applications/science/biology/astral/make-deterministic.patch new file mode 100644 index 000000000000..940182e2f49f --- /dev/null +++ b/pkgs/applications/science/biology/astral/make-deterministic.patch @@ -0,0 +1,21 @@ +diff --git a/make.sh b/make.sh +index 3ff6529..937b1a2 100644 +--- a/make.sh ++++ b/make.sh +@@ -17,6 +17,8 @@ jar cvfm ../astral.$version.jar ../manifest.text phylonet/util/BitSet.* phylonet + + cd .. + ++strip-nondeterminism --type jar astral.$version.jar ++ + chmod +x astral.$version.jar + sed -e "s/__astral.jar__/astral.$version.jar/g" -e "s/__astral.zip__/Astral.$version.zip/g" README.template.md > README.md + sed -e "s/__astral.jar__/astral.$version.jar/g" -e "s/__astral.zip__/Astral.$version.zip/g" astral-tutorial-template.md > astral-tutorial.md +@@ -32,6 +34,7 @@ ln -s ../astral-tutorial.pdf . + cd .. + rm -f Astral.$version.zip + zip -r Astral.$version.zip Astral ++strip-nondeterminism --type zip Astral.$version.zip + + set +x + echo " diff --git a/pkgs/applications/science/biology/bamtools/default.nix b/pkgs/applications/science/biology/bamtools/default.nix index 05373dafd381..602254e2966a 100644 --- a/pkgs/applications/science/biology/bamtools/default.nix +++ b/pkgs/applications/science/biology/bamtools/default.nix @@ -32,6 +32,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { 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/${finalAttrs.src.rev}"; license = licenses.mit; diff --git a/pkgs/applications/science/biology/bioawk/default.nix b/pkgs/applications/science/biology/bioawk/default.nix index cfbb1a551fac..f7da30fc4f72 100644 --- a/pkgs/applications/science/biology/bioawk/default.nix +++ b/pkgs/applications/science/biology/bioawk/default.nix @@ -42,6 +42,7 @@ stdenv.mkDerivation { meta = with lib; { description = "BWK awk modified for biological data"; + mainProgram = "bioawk"; homepage = "https://github.com/lh3/bioawk"; license = licenses.hpnd; maintainers = with maintainers; [ natsukium ]; diff --git a/pkgs/applications/science/biology/bwa-mem2/default.nix b/pkgs/applications/science/biology/bwa-mem2/default.nix index b34b6dc8c90f..c339baf446d2 100644 --- a/pkgs/applications/science/biology/bwa-mem2/default.nix +++ b/pkgs/applications/science/biology/bwa-mem2/default.nix @@ -46,6 +46,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Next version of the bwa-mem algorithm in bwa, a software package for mapping low-divergent sequences against a large reference genome"; + mainProgram = "bwa-mem2"; license = licenses.mit; homepage = "https://github.com/bwa-mem2/bwa-mem2/"; changelog = "https://github.com/bwa-mem2/bwa-mem2/blob/${finalAttrs.src.rev}/NEWS.md"; diff --git a/pkgs/applications/science/biology/bwa/default.nix b/pkgs/applications/science/biology/bwa/default.nix index 4786f25beb50..8c883e2617bf 100644 --- a/pkgs/applications/science/biology/bwa/default.nix +++ b/pkgs/applications/science/biology/bwa/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation { meta = with lib; { description = "A software package for mapping low-divergent sequences against a large reference genome, such as the human genome"; + mainProgram = "bwa"; license = licenses.gpl3Plus; homepage = "https://bio-bwa.sourceforge.net/"; maintainers = with maintainers; [ luispedro ]; diff --git a/pkgs/applications/science/biology/cmtk/default.nix b/pkgs/applications/science/biology/cmtk/default.nix index a131c6645499..d7d23dd2d46e 100644 --- a/pkgs/applications/science/biology/cmtk/default.nix +++ b/pkgs/applications/science/biology/cmtk/default.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Computational Morphometry Toolkit"; + mainProgram = "cmtk"; longDescription = ''A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O''; diff --git a/pkgs/applications/science/biology/conglomerate/default.nix b/pkgs/applications/science/biology/conglomerate/default.nix index fe1c1f5511d1..d9092b9eeb11 100644 --- a/pkgs/applications/science/biology/conglomerate/default.nix +++ b/pkgs/applications/science/biology/conglomerate/default.nix @@ -32,6 +32,6 @@ stdenv.mkDerivation rec { description = "More command-line utilities for working with MINC files"; maintainers = with maintainers; [ bcdarwin ]; platforms = platforms.unix; - license = licenses.free; + license = licenses.hpndUc; }; } diff --git a/pkgs/applications/science/biology/dcm2niix/default.nix b/pkgs/applications/science/biology/dcm2niix/default.nix index 605ecaadf648..a7f30dbc075d 100644 --- a/pkgs/applications/science/biology/dcm2niix/default.nix +++ b/pkgs/applications/science/biology/dcm2niix/default.nix @@ -57,6 +57,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "DICOM to NIfTI converter"; + mainProgram = "dcm2niix"; longDescription = '' dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. ''; diff --git a/pkgs/applications/science/biology/deeptools/default.nix b/pkgs/applications/science/biology/deeptools/default.nix index a7a1f77dfe90..2abd0825e6e3 100644 --- a/pkgs/applications/science/biology/deeptools/default.nix +++ b/pkgs/applications/science/biology/deeptools/default.nix @@ -5,14 +5,14 @@ python3.pkgs.buildPythonApplication rec { pname = "deeptools"; - version = "3.5.4"; + version = "3.5.5"; pyproject = true; src = fetchFromGitHub { owner = "deeptools"; repo = "deepTools"; - rev = version; - hash = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI="; + rev = "refs/tags/${version}"; + hash = "sha256-2kSlL7Y5f/FjVtStnmz+GlTw2oymrtxOCaXlqgbQ7FU="; }; nativeBuildInputs = with python3.pkgs; [ diff --git a/pkgs/applications/science/biology/delly/default.nix b/pkgs/applications/science/biology/delly/default.nix index b483b3d57bef..34ea942b4f5c 100644 --- a/pkgs/applications/science/biology/delly/default.nix +++ b/pkgs/applications/science/biology/delly/default.nix @@ -54,6 +54,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Structural variant caller for mapped DNA sequenced data"; + mainProgram = "delly"; license = licenses.bsd3; maintainers = with maintainers; [ scalavision ]; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/diamond/default.nix b/pkgs/applications/science/biology/diamond/default.nix index 3349c0392d08..f3afff0f5eb7 100644 --- a/pkgs/applications/science/biology/diamond/default.nix +++ b/pkgs/applications/science/biology/diamond/default.nix @@ -17,6 +17,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Accelerated BLAST compatible local sequence aligner"; + mainProgram = "diamond"; longDescription = '' DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. The key features are: - Pairwise alignment of proteins and translated DNA at 100x-10,000x speed of BLAST. diff --git a/pkgs/applications/science/biology/dssp/default.nix b/pkgs/applications/science/biology/dssp/default.nix index 006b46db9974..6c7157a91764 100644 --- a/pkgs/applications/science/biology/dssp/default.nix +++ b/pkgs/applications/science/biology/dssp/default.nix @@ -51,6 +51,7 @@ stdenv.mkDerivation (finalAttrs: { meta = with lib; { description = "Calculate the most likely secondary structure assignment given the 3D structure of a protein"; + mainProgram = "mkdssp"; homepage = "https://github.com/PDB-REDO/dssp"; changelog = "https://github.com/PDB-REDO/libcifpp/releases/tag/${finalAttrs.src.rev}"; license = licenses.bsd2; diff --git a/pkgs/applications/science/biology/est-sfs/default.nix b/pkgs/applications/science/biology/est-sfs/default.nix index fe4a3e49930c..c306cfd71c39 100644 --- a/pkgs/applications/science/biology/est-sfs/default.nix +++ b/pkgs/applications/science/biology/est-sfs/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "https://sourceforge.net/projects/est-usfs"; description = "Estimate the unfolded site frequency spectrum and ancestral states"; + mainProgram = "est-sfs"; license = licenses.gpl3; maintainers = [ maintainers.bzizou ]; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/fastp/default.nix b/pkgs/applications/science/biology/fastp/default.nix index e7fc0d4a35f1..0495da0e3c3d 100644 --- a/pkgs/applications/science/biology/fastp/default.nix +++ b/pkgs/applications/science/biology/fastp/default.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Ultra-fast all-in-one FASTQ preprocessor"; + mainProgram = "fastp"; license = licenses.mit; homepage = "https://github.com/OpenGene/fastp"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/febio-studio/default.nix b/pkgs/applications/science/biology/febio-studio/default.nix index 550d221c74eb..708bd0f4305a 100644 --- a/pkgs/applications/science/biology/febio-studio/default.nix +++ b/pkgs/applications/science/biology/febio-studio/default.nix @@ -53,6 +53,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "FEBio Suite Solver"; + mainProgram = "FEBioStudio"; license = with licenses; [ mit ]; homepage = "https://febio.org/"; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/flywheel-cli/default.nix b/pkgs/applications/science/biology/flywheel-cli/default.nix index 254a3c011d27..51600d31c513 100644 --- a/pkgs/applications/science/biology/flywheel-cli/default.nix +++ b/pkgs/applications/science/biology/flywheel-cli/default.nix @@ -41,6 +41,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Library and command line interface for interacting with a Flywheel site"; + mainProgram = "fw"; homepage = "https://gitlab.com/flywheel-io/public/python-cli"; sourceProvenance = with sourceTypes; [ binaryNativeCode ]; license = licenses.mit; diff --git a/pkgs/applications/science/biology/genmap/default.nix b/pkgs/applications/science/biology/genmap/default.nix index c6f9cf1fb193..235135cb6050 100644 --- a/pkgs/applications/science/biology/genmap/default.nix +++ b/pkgs/applications/science/biology/genmap/default.nix @@ -32,6 +32,7 @@ stdenv.mkDerivation rec { meta = { description = "Ultra-fast computation of genome mappability"; + mainProgram = "genmap"; license = lib.licenses.bsd3; homepage = "https://github.com/cpockrandt/genmap"; maintainers = with lib.maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/iqtree/default.nix b/pkgs/applications/science/biology/iqtree/default.nix index 37a8a58a92e1..17b2ba9f9bde 100644 --- a/pkgs/applications/science/biology/iqtree/default.nix +++ b/pkgs/applications/science/biology/iqtree/default.nix @@ -33,6 +33,7 @@ stdenv.mkDerivation rec { meta = with lib; { homepage = "http://www.iqtree.org/"; description = "Efficient and versatile phylogenomic software by maximum likelihood"; + mainProgram = "iqtree2"; license = licenses.lgpl2; maintainers = with maintainers; [ bzizou ]; platforms = [ "x86_64-linux" "x86_64-darwin" ]; diff --git a/pkgs/applications/science/biology/itsx/default.nix b/pkgs/applications/science/biology/itsx/default.nix index 843f0df57924..366b4add2ed7 100644 --- a/pkgs/applications/science/biology/itsx/default.nix +++ b/pkgs/applications/science/biology/itsx/default.nix @@ -26,6 +26,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing"; + mainProgram = "ITSx"; homepage = "https://microbiology.se/software/itsx/"; license = licenses.gpl3; maintainers = [ maintainers.bzizou ]; diff --git a/pkgs/applications/science/biology/jbrowse/default.nix b/pkgs/applications/science/biology/jbrowse/default.nix index 3ed6a885aa75..15694ae3e638 100644 --- a/pkgs/applications/science/biology/jbrowse/default.nix +++ b/pkgs/applications/science/biology/jbrowse/default.nix @@ -31,6 +31,7 @@ appimageTools.wrapType2 { meta = with lib; { description = "The next-generation genome browser"; + mainProgram = "jbrowse-desktop"; homepage = "https://jbrowse.org/jb2/"; license = licenses.asl20; maintainers = with maintainers; [ benwbooth ]; diff --git a/pkgs/applications/science/biology/kalign/default.nix b/pkgs/applications/science/biology/kalign/default.nix index 3ca83978d969..f26b679f799d 100644 --- a/pkgs/applications/science/biology/kalign/default.nix +++ b/pkgs/applications/science/biology/kalign/default.nix @@ -37,6 +37,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { description = "A fast multiple sequence alignment program"; + mainProgram = "kalign"; homepage = "https://github.com/TimoLassmann/kalign"; changelog = "https://github.com/TimoLassmann/kalign/releases/tag/${finalAttrs.src.rev}"; license = lib.licenses.gpl3Plus; diff --git a/pkgs/applications/science/biology/kallisto/default.nix b/pkgs/applications/science/biology/kallisto/default.nix index a193fa59238f..55c555e387de 100644 --- a/pkgs/applications/science/biology/kallisto/default.nix +++ b/pkgs/applications/science/biology/kallisto/default.nix @@ -22,6 +22,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Program for quantifying abundances of transcripts from RNA-Seq data"; + mainProgram = "kallisto"; homepage = "https://pachterlab.github.io/kallisto"; license = licenses.bsd2; platforms = platforms.linux; diff --git a/pkgs/applications/science/biology/macs2/default.nix b/pkgs/applications/science/biology/macs2/default.nix index 8884d41d9064..73f12af6a605 100644 --- a/pkgs/applications/science/biology/macs2/default.nix +++ b/pkgs/applications/science/biology/macs2/default.nix @@ -46,6 +46,7 @@ python3.pkgs.buildPythonPackage rec { meta = with lib; { description = "Model-based Analysis for ChIP-Seq"; + mainProgram = "macs2"; homepage = "https://github.com/macs3-project/MACS/"; changelog = "https://github.com/macs3-project/MACS/releases/tag/v${version}"; license = licenses.bsd3; diff --git a/pkgs/applications/science/biology/macse/default.nix b/pkgs/applications/science/biology/macse/default.nix index 2ac09ca21ab6..06937f7e645e 100644 --- a/pkgs/applications/science/biology/macse/default.nix +++ b/pkgs/applications/science/biology/macse/default.nix @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Multiple alignment of coding sequences"; + mainProgram = "macse"; homepage = "https://bioweb.supagro.inra.fr/macse/"; sourceProvenance = with sourceTypes; [ binaryBytecode ]; license = licenses.gpl2; diff --git a/pkgs/applications/science/biology/mafft/default.nix b/pkgs/applications/science/biology/mafft/default.nix index e9acd1c88b66..f2e3ead2e913 100644 --- a/pkgs/applications/science/biology/mafft/default.nix +++ b/pkgs/applications/science/biology/mafft/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "mafft"; - version = "7.520"; + version = "7.525"; src = fetchFromGitLab { owner = "sysimm"; repo = pname; rev = "v${version}"; - sha256 = "sha256-H+EcKahJWwidAx+IUT4uCZEty+S8hUeMSB8VbTu5SmQ="; + sha256 = "sha256-ckBmvFssYAmYcBHAEftjQqBV0MB0theGfemaPx3XUws="; }; preBuild = '' diff --git a/pkgs/applications/science/biology/minia/default.nix b/pkgs/applications/science/biology/minia/default.nix index 023a05d7504f..3665639a2cd9 100644 --- a/pkgs/applications/science/biology/minia/default.nix +++ b/pkgs/applications/science/biology/minia/default.nix @@ -25,8 +25,9 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Short read genome assembler"; + mainProgram = "minia"; homepage = "https://github.com/GATB/minia"; - license = licenses.agpl3; + license = licenses.agpl3Plus; maintainers = with maintainers; [ jbedo ]; platforms = [ "x86_64-linux" ]; }; diff --git a/pkgs/applications/science/biology/minimap2/default.nix b/pkgs/applications/science/biology/minimap2/default.nix index 35c1b076d7eb..eeb31dee0538 100644 --- a/pkgs/applications/science/biology/minimap2/default.nix +++ b/pkgs/applications/science/biology/minimap2/default.nix @@ -2,13 +2,13 @@ stdenv.mkDerivation rec { pname = "minimap2"; - version = "2.26"; + version = "2.27"; src = fetchFromGitHub { repo = pname; owner = "lh3"; rev = "v${version}"; - sha256 = "sha256-vK8Z/j6Ndu1vMFYPPzViP4evtIhyVVFwsfTqNCYnXpQ="; + sha256 = "sha256-F6IJrYD2dk+5bKKVIahLiNnD/Hd/CjNQQd9zz0Gkans="; }; buildInputs = [ zlib ]; @@ -24,6 +24,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "A versatile pairwise aligner for genomic and spliced nucleotide sequences"; + mainProgram = "minimap2"; homepage = "https://lh3.github.io/minimap2"; license = licenses.mit; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/mmseqs2/default.nix b/pkgs/applications/science/biology/mmseqs2/default.nix index 3e39fcb2918b..18acee7a5f14 100644 --- a/pkgs/applications/science/biology/mmseqs2/default.nix +++ b/pkgs/applications/science/biology/mmseqs2/default.nix @@ -42,6 +42,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Ultra fast and sensitive sequence search and clustering suite"; + mainProgram = "mmseqs"; homepage = "https://mmseqs.com/"; license = licenses.gpl3; maintainers = with maintainers; [ natsukium ]; diff --git a/pkgs/applications/science/biology/mrbayes/default.nix b/pkgs/applications/science/biology/mrbayes/default.nix index e4c2bbe65652..54f5b9bbb370 100644 --- a/pkgs/applications/science/biology/mrbayes/default.nix +++ b/pkgs/applications/science/biology/mrbayes/default.nix @@ -13,6 +13,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Bayesian Inference of Phylogeny"; + mainProgram = "mb"; longDescription = '' Bayesian inference of phylogeny is based upon a quantity called the posterior probability distribution of trees, which is diff --git a/pkgs/applications/science/biology/muscle/default.nix b/pkgs/applications/science/biology/muscle/default.nix index 366d0278227d..cdcf6c7b50aa 100644 --- a/pkgs/applications/science/biology/muscle/default.nix +++ b/pkgs/applications/science/biology/muscle/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { 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/"; maintainers = with maintainers; [ unode thyol ]; diff --git a/pkgs/applications/science/biology/obitools/obitools3.nix b/pkgs/applications/science/biology/obitools/obitools3.nix index 9bf579a80c3b..f415c9c39141 100644 --- a/pkgs/applications/science/biology/obitools/obitools3.nix +++ b/pkgs/applications/science/biology/obitools/obitools3.nix @@ -27,6 +27,7 @@ python3Packages.buildPythonApplication rec { meta = with lib ; { description = "Management of analyses and data in DNA metabarcoding"; + mainProgram = "obi"; homepage = "https://git.metabarcoding.org/obitools/obitools3"; license = licenses.cecill20; maintainers = [ maintainers.bzizou ]; diff --git a/pkgs/applications/science/biology/octopus/default.nix b/pkgs/applications/science/biology/octopus/default.nix index 0090ca82d6c3..c594108c6f47 100644 --- a/pkgs/applications/science/biology/octopus/default.nix +++ b/pkgs/applications/science/biology/octopus/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Bayesian haplotype-based mutation calling"; + mainProgram = "octopus"; license = licenses.mit; homepage = "https://github.com/luntergroup/octopus"; 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 00fd0ff0083e..0e65bed4cf3e 100644 --- a/pkgs/applications/science/biology/plink-ng/default.nix +++ b/pkgs/applications/science/biology/plink-ng/default.nix @@ -33,6 +33,7 @@ stdenv.mkDerivation rec { meta = { broken = (stdenv.isLinux && stdenv.isAarch64); description = "A comprehensive update to the PLINK association analysis toolset"; + mainProgram = "plink"; homepage = "https://www.cog-genomics.org/plink2"; license = lib.licenses.gpl3; platforms = lib.platforms.linux; diff --git a/pkgs/applications/science/biology/prodigal/default.nix b/pkgs/applications/science/biology/prodigal/default.nix index 28a21522c6b8..cd83a723f91e 100644 --- a/pkgs/applications/science/biology/prodigal/default.nix +++ b/pkgs/applications/science/biology/prodigal/default.nix @@ -18,6 +18,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Fast, reliable protein-coding gene prediction for prokaryotic genomes"; + mainProgram = "prodigal"; homepage = "https://github.com/hyattpd/Prodigal"; license = licenses.gpl3; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/repseek/default.nix b/pkgs/applications/science/biology/repseek/default.nix index 5966c83b7a5f..e5e0193f7911 100644 --- a/pkgs/applications/science/biology/repseek/default.nix +++ b/pkgs/applications/science/biology/repseek/default.nix @@ -19,6 +19,7 @@ stdenv.mkDerivation rec { meta = { description = "Tool to retrieve approximate repeats from large DNA sequences"; + mainProgram = "repseek"; homepage = "https://bioinfo.mnhn.fr/abi/public/RepSeek"; maintainers = [ lib.maintainers.bzizou ]; license = lib.licenses.lgpl21; diff --git a/pkgs/applications/science/biology/sambamba/default.nix b/pkgs/applications/science/biology/sambamba/default.nix index e1722a7086d8..b6635f02aacd 100644 --- a/pkgs/applications/science/biology/sambamba/default.nix +++ b/pkgs/applications/science/biology/sambamba/default.nix @@ -38,6 +38,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "SAM/BAM processing tool"; + mainProgram = "sambamba"; homepage = "https://lomereiter.github.io/sambamba/"; maintainers = with maintainers; [ jbedo ]; license = with licenses; gpl2; diff --git a/pkgs/applications/science/biology/samblaster/default.nix b/pkgs/applications/science/biology/samblaster/default.nix index 4315dd2767e1..f16d0e42d8ef 100644 --- a/pkgs/applications/science/biology/samblaster/default.nix +++ b/pkgs/applications/science/biology/samblaster/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Tool for marking duplicates and extracting discordant/split reads from SAM/BAM files"; + mainProgram = "samblaster"; maintainers = with maintainers; [ jbedo ]; license = licenses.mit; homepage = "https://github.com/GregoryFaust/samblaster"; diff --git a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix index 2472e4976cad..edb3a9a9da5b 100644 --- a/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix +++ b/pkgs/applications/science/biology/samtools/samtools_0_1_19.nix @@ -25,6 +25,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Tools for manipulating SAM/BAM/CRAM format"; + mainProgram = "samtools"; license = licenses.mit; homepage = "https://samtools.sourceforge.net/"; platforms = platforms.unix; diff --git a/pkgs/applications/science/biology/seaview/default.nix b/pkgs/applications/science/biology/seaview/default.nix index 640d2f5ae416..06549748018d 100644 --- a/pkgs/applications/science/biology/seaview/default.nix +++ b/pkgs/applications/science/biology/seaview/default.nix @@ -16,6 +16,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "GUI for molecular phylogeny"; + mainProgram = "seaview"; longDescription = '' SeaView is a multiplatform, graphical user interface for multiple sequence alignment and molecular phylogeny. - SeaView reads and writes various file formats (NEXUS, MSF, CLUSTAL, FASTA, PHYLIP, MASE, Newick) of DNA and protein sequences and of phylogenetic trees. diff --git a/pkgs/applications/science/biology/seqtk/default.nix b/pkgs/applications/science/biology/seqtk/default.nix index 90bd4bb3c65e..417bec9c062f 100644 --- a/pkgs/applications/science/biology/seqtk/default.nix +++ b/pkgs/applications/science/biology/seqtk/default.nix @@ -31,6 +31,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Toolkit for processing sequences in FASTA/Q formats"; + mainProgram = "seqtk"; license = licenses.mit; homepage = "https://github.com/lh3/seqtk"; platforms = platforms.all; diff --git a/pkgs/applications/science/biology/somatic-sniper/default.nix b/pkgs/applications/science/biology/somatic-sniper/default.nix index 034409cfb013..553725fb4566 100644 --- a/pkgs/applications/science/biology/somatic-sniper/default.nix +++ b/pkgs/applications/science/biology/somatic-sniper/default.nix @@ -20,6 +20,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Identify single nucleotide positions that are different between tumor and normal"; + mainProgram = "bam-somaticsniper"; license = licenses.mit; homepage = "https://github.com/genome/somatic-sniper"; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/sortmerna/default.nix b/pkgs/applications/science/biology/sortmerna/default.nix index bfd6d20f1384..d47aae9ce665 100644 --- a/pkgs/applications/science/biology/sortmerna/default.nix +++ b/pkgs/applications/science/biology/sortmerna/default.nix @@ -40,6 +40,7 @@ stdenv.mkDerivation rec { meta = with lib; { description = "Tools for filtering, mapping, and OTU-picking from shotgun genomics data"; + mainProgram = "sortmerna"; license = licenses.lgpl3; platforms = platforms.x86_64; homepage = "https://bioinfo.lifl.fr/RNA/sortmerna/"; diff --git a/pkgs/applications/science/biology/svaba/default.nix b/pkgs/applications/science/biology/svaba/default.nix index d36c4b668ec3..fec5a5a3b92d 100644 --- a/pkgs/applications/science/biology/svaba/default.nix +++ b/pkgs/applications/science/biology/svaba/default.nix @@ -36,6 +36,7 @@ stdenv.mkDerivation rec { meta = with lib; { broken = (stdenv.isLinux && stdenv.isAarch64); description = "Structural variant and INDEL caller for DNA sequencing data, using genome-wide local assembly"; + mainProgram = "svaba"; license = licenses.gpl3; homepage = "https://github.com/walaj/svaba"; maintainers = with maintainers; [ scalavision ]; diff --git a/pkgs/applications/science/biology/tebreak/default.nix b/pkgs/applications/science/biology/tebreak/default.nix index a046aee1c6c3..879f9b95d846 100644 --- a/pkgs/applications/science/biology/tebreak/default.nix +++ b/pkgs/applications/science/biology/tebreak/default.nix @@ -40,6 +40,7 @@ python3.pkgs.buildPythonApplication rec { meta = with lib; { description = "Find and characterise transposable element insertions"; + mainProgram = "tebreak"; homepage = "https://github.com/adamewing/tebreak"; license = licenses.mit; maintainers = with maintainers; [ jbedo ]; diff --git a/pkgs/applications/science/biology/trimmomatic/default.nix b/pkgs/applications/science/biology/trimmomatic/default.nix index 53cff76badce..db19278eaa47 100644 --- a/pkgs/applications/science/biology/trimmomatic/default.nix +++ b/pkgs/applications/science/biology/trimmomatic/default.nix @@ -5,7 +5,7 @@ , jdk , jre , makeWrapper -, canonicalize-jars-hook +, stripJavaArchivesHook }: stdenv.mkDerivation (finalAttrs: { @@ -29,7 +29,7 @@ stdenv.mkDerivation (finalAttrs: { ant jdk makeWrapper - canonicalize-jars-hook + stripJavaArchivesHook ]; buildPhase = '' diff --git a/pkgs/applications/science/biology/veryfasttree/default.nix b/pkgs/applications/science/biology/veryfasttree/default.nix index 63597a75d494..6c054fecd742 100644 --- a/pkgs/applications/science/biology/veryfasttree/default.nix +++ b/pkgs/applications/science/biology/veryfasttree/default.nix @@ -29,6 +29,7 @@ stdenv.mkDerivation (finalAttrs: { meta = { description = "Speeding up the estimation of phylogenetic trees for large alignments through parallelization and vectorization strategies"; + mainProgram = "VeryFastTree"; homepage = "https://github.com/citiususc/veryfasttree"; license = lib.licenses.gpl3Plus; maintainers = with lib.maintainers; [ thyol ]; |