diff options
-rw-r--r-- | pkgs/applications/science/biology/picard-tools/default.nix | 30 | ||||
-rw-r--r-- | pkgs/top-level/all-packages.nix | 2 |
2 files changed, 32 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix new file mode 100644 index 000000000000..3f17825202ea --- /dev/null +++ b/pkgs/applications/science/biology/picard-tools/default.nix @@ -0,0 +1,30 @@ +{stdenv, fetchurl, jre, makeWrapper}: + +stdenv.mkDerivation rec { + name = "picard-tools-${version}"; + version = "2.7.1"; + + src = fetchurl { + url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar"; + sha256 = "0rcfcvy9zacqmh7nyqlm93hzsx6gfygmcf8d2p02h5l69gvygnb9"; + }; + + buildInputs = [ jre makeWrapper ]; + + phases = [ "installPhase" ]; + + installPhase = '' + mkdir -p $out/libexec/picard + cp $src $out/libexec/picard/picard.jar + mkdir -p $out/bin + makeWrapper ${jre}/bin/java $out/bin/picard --add-flags "-jar $out/libexec/picard/picard.jar" + ''; + + meta = with stdenv.lib; { + description = "Tools for high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF."; + license = licenses.mit; + homepage = https://broadinstitute.github.io/picard/; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.all; + }; +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index b3b78bf18279..47e75c8632a2 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -16998,6 +16998,8 @@ with pkgs; paml = callPackage ../applications/science/biology/paml { }; + picard-tools = callPackage ../applications/science/biology/picard-tools/default.nix { }; + platypus = callPackage ../applications/science/biology/platypus/default.nix { }; plink = callPackage ../applications/science/biology/plink/default.nix { }; |