diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
4 files changed, 70 insertions, 5 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/blast/default.nix b/nixpkgs/pkgs/applications/science/biology/blast/default.nix index 383aa6d09a5b..407d38970b0f 100644 --- a/nixpkgs/pkgs/applications/science/biology/blast/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/blast/default.nix @@ -2,11 +2,11 @@ stdenv.mkDerivation rec { pname = "blast"; - version = "2.14.0"; + version = "2.14.1"; src = fetchurl { url = "https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${version}/ncbi-blast-${version}+-src.tar.gz"; - sha256 = "sha256-v0d/Gww7gvC3pwlL8AOpqD4347BxbB33mQYMT+qxdQA="; + sha256 = "sha256-cSwtvfD7E8wcLU9O9d0c5LBsO1fpbf6o8j5umfWxZQ4="; }; sourceRoot = "ncbi-blast-${version}+-src/c++"; diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix index b36104bcf769..f2825eeb97be 100644 --- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix @@ -2,14 +2,14 @@ nimPackages.buildNimPackage rec { pname = "mosdepth"; - version = "0.3.4"; + version = "0.3.5"; nimBinOnly = true; src = fetchFromGitHub { owner = "brentp"; repo = "mosdepth"; rev = "v${version}"; - sha256 = "sha256-7uteYTCbAaXedPqk0WtHpqTfUWH/+rRW8aSlFixkEko="; + sha256 = "sha256-tG3J51PS6A0WBCZ+j/Nf7aaukFV+DZJsxpbTbvwu0zc="; }; buildInputs = [ docopt hts pcre ]; diff --git a/nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix b/nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix index 6884e1955f75..a529867aaa74 100644 --- a/nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix +++ b/nixpkgs/pkgs/applications/science/biology/sortmerna/default.nix @@ -15,7 +15,6 @@ stdenv.mkDerivation rec { buildInputs = [ zlib rocksdb rapidjson ]; cmakeFlags = [ - "-DCMAKE_BUILD_TYPE=Release" "-DPORTABLE=off" "-DRAPIDJSON_HOME=${rapidjson}" "-DROCKSDB_HOME=${rocksdb}" diff --git a/nixpkgs/pkgs/applications/science/biology/trimmomatic/default.nix b/nixpkgs/pkgs/applications/science/biology/trimmomatic/default.nix new file mode 100644 index 000000000000..ad1dc45c5c26 --- /dev/null +++ b/nixpkgs/pkgs/applications/science/biology/trimmomatic/default.nix @@ -0,0 +1,66 @@ +{ lib +, stdenv +, ant +, fetchFromGitHub +, jdk11_headless +, jre +, makeWrapper +}: + +stdenv.mkDerivation rec { + pname = "trimmomatic"; + version = "0.39"; + + src = fetchFromGitHub { + owner = "usadellab"; + repo = "Trimmomatic"; + rev = "v${version}"; + hash = "sha256-u+ubmacwPy/vsEi0YQCv0fTnVDesQvqeQDEwCbS8M6I="; + }; + + # Set source and target version to 11 + postPatch = '' + substituteInPlace ./build.xml \ + --replace 'source="1.5" target="1.5"' 'release="11"' + ''; + + nativeBuildInputs = [ jdk11_headless ant makeWrapper ]; + + buildPhase = '' + runHook preBuild + + ant + + runHook postBuild + ''; + + installPhase = '' + runHook preInstall + + mkdir -p $out/bin $out/share + cp dist/jar/trimmomatic-${version}.jar $out/share/ + cp -r adapters $out/share/ + makeWrapper ${jre}/bin/java $out/bin/trimmomatic \ + --add-flags "-cp $out/share/trimmomatic-${version}.jar org.usadellab.trimmomatic.Trimmomatic" + + runHook postInstall + ''; + + meta = { + description = "A flexible read trimming tool for Illumina NGS data"; + longDescription = '' + Trimmomatic performs a variety of useful trimming tasks for illumina + paired-end and single ended data: adapter trimming, quality trimming, + cropping to a specified length, length filtering, quality score + conversion. + ''; + homepage = "http://www.usadellab.org/cms/?page=trimmomatic"; + downloadPage = "https://github.com/usadellab/Trimmomatic/releases"; + license = lib.licenses.gpl3Only; + sourceProvenance = [ + lib.sourceTypes.fromSource + lib.sourceTypes.binaryBytecode # source bundles dependencies as jars + ]; + maintainers = [ lib.maintainers.kupac ]; + }; +} |