diff options
author | Alyssa Ross <hi@alyssa.is> | 2024-01-20 12:31:50 +0100 |
---|---|---|
committer | Alyssa Ross <hi@alyssa.is> | 2024-01-20 12:32:25 +0100 |
commit | b7baf40e099b4215181fe7b0c63083b12ef2c7fb (patch) | |
tree | a6efabd31d05b6d0a36624729e80377bbbfb0149 /nixpkgs/pkgs/applications/science/biology | |
parent | 710028664e26e85cb831a869b3da9f6993902255 (diff) | |
parent | 0799f514b1cd74878174939df79ac60ca5036673 (diff) | |
download | nixlib-b7baf40e099b4215181fe7b0c63083b12ef2c7fb.tar nixlib-b7baf40e099b4215181fe7b0c63083b12ef2c7fb.tar.gz nixlib-b7baf40e099b4215181fe7b0c63083b12ef2c7fb.tar.bz2 nixlib-b7baf40e099b4215181fe7b0c63083b12ef2c7fb.tar.lz nixlib-b7baf40e099b4215181fe7b0c63083b12ef2c7fb.tar.xz nixlib-b7baf40e099b4215181fe7b0c63083b12ef2c7fb.tar.zst nixlib-b7baf40e099b4215181fe7b0c63083b12ef2c7fb.zip |
Merge branch 'nixos-unstable-small' of https://github.com/NixOS/nixpkgs
Conflicts: nixpkgs/pkgs/build-support/rust/build-rust-package/default.nix
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
-rw-r--r-- | nixpkgs/pkgs/applications/science/biology/igv/default.nix | 4 | ||||
-rw-r--r-- | nixpkgs/pkgs/applications/science/biology/trimmomatic/default.nix | 34 |
2 files changed, 23 insertions, 15 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/igv/default.nix b/nixpkgs/pkgs/applications/science/biology/igv/default.nix index a74208c706a1..827fdb6fa1ab 100644 --- a/nixpkgs/pkgs/applications/science/biology/igv/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/igv/default.nix @@ -2,10 +2,10 @@ stdenv.mkDerivation rec { pname = "igv"; - version = "2.16.2"; + version = "2.17.0"; src = fetchzip { url = "https://data.broadinstitute.org/igv/projects/downloads/${lib.versions.majorMinor version}/IGV_${version}.zip"; - sha256 = "sha256-/X9loW8rOevf/GA/Wk3bVsES9ZceF79Bkwby75SJgTQ="; + sha256 = "sha256-nOwaeVIvqfHrvykfTyOdnMN6+QpsvNN14jXBQx7THsE="; }; installPhase = '' diff --git a/nixpkgs/pkgs/applications/science/biology/trimmomatic/default.nix b/nixpkgs/pkgs/applications/science/biology/trimmomatic/default.nix index ad1dc45c5c26..53cff76badce 100644 --- a/nixpkgs/pkgs/applications/science/biology/trimmomatic/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/trimmomatic/default.nix @@ -1,30 +1,36 @@ { lib , stdenv -, ant , fetchFromGitHub -, jdk11_headless +, ant +, jdk , jre , makeWrapper +, canonicalize-jars-hook }: -stdenv.mkDerivation rec { +stdenv.mkDerivation (finalAttrs: { pname = "trimmomatic"; version = "0.39"; src = fetchFromGitHub { owner = "usadellab"; repo = "Trimmomatic"; - rev = "v${version}"; + rev = "v${finalAttrs.version}"; hash = "sha256-u+ubmacwPy/vsEi0YQCv0fTnVDesQvqeQDEwCbS8M6I="; }; - # Set source and target version to 11 + # Remove jdk version requirement postPatch = '' substituteInPlace ./build.xml \ - --replace 'source="1.5" target="1.5"' 'release="11"' + --replace 'source="1.5" target="1.5"' "" ''; - nativeBuildInputs = [ jdk11_headless ant makeWrapper ]; + nativeBuildInputs = [ + ant + jdk + makeWrapper + canonicalize-jars-hook + ]; buildPhase = '' runHook preBuild @@ -37,16 +43,17 @@ stdenv.mkDerivation rec { installPhase = '' runHook preInstall - mkdir -p $out/bin $out/share - cp dist/jar/trimmomatic-${version}.jar $out/share/ - cp -r adapters $out/share/ + install -Dm644 dist/jar/trimmomatic-*.jar -t $out/share/trimmomatic + cp -r adapters $out/share/trimmomatic + makeWrapper ${jre}/bin/java $out/bin/trimmomatic \ - --add-flags "-cp $out/share/trimmomatic-${version}.jar org.usadellab.trimmomatic.Trimmomatic" + --add-flags "-jar $out/share/trimmomatic/trimmomatic-*.jar" runHook postInstall ''; meta = { + changelog = "https://github.com/usadellab/Trimmomatic/blob/main/versionHistory.txt"; description = "A flexible read trimming tool for Illumina NGS data"; longDescription = '' Trimmomatic performs a variety of useful trimming tasks for illumina @@ -59,8 +66,9 @@ stdenv.mkDerivation rec { license = lib.licenses.gpl3Only; sourceProvenance = [ lib.sourceTypes.fromSource - lib.sourceTypes.binaryBytecode # source bundles dependencies as jars + lib.sourceTypes.binaryBytecode # source bundles dependencies as jars ]; + mainProgram = "trimmomatic"; maintainers = [ lib.maintainers.kupac ]; }; -} +}) |