diff options
| -rw-r--r-- | pkgs/applications/science/biology/snpeff/default.nix | 31 | ||||
| -rw-r--r-- | pkgs/top-level/all-packages.nix | 2 |
2 files changed, 33 insertions, 0 deletions
diff --git a/pkgs/applications/science/biology/snpeff/default.nix b/pkgs/applications/science/biology/snpeff/default.nix new file mode 100644 index 000000000000..6c7a6b969ee6 --- /dev/null +++ b/pkgs/applications/science/biology/snpeff/default.nix @@ -0,0 +1,31 @@ +{stdenv, fetchurl, jre, unzip, makeWrapper}: + +stdenv.mkDerivation rec { + name = "snpeff-${version}"; + version = "4.3i"; + + src = fetchurl { + url = "mirror://sourceforge/project/snpeff/snpEff_latest_core.zip"; + sha256 = "0i1slg201c8yjfr4wrg4xcgzwi0c8b9l3fb1i73fphq6q6zdblzb"; + }; + + buildInputs = [ unzip jre makeWrapper ]; + + installPhase = '' + mkdir -p $out/libexec/snpeff + cp *.jar *.config $out/libexec/snpeff + + mkdir -p $out/bin + makeWrapper ${jre}/bin/java $out/bin/snpeff --add-flags "-jar $out/libexec/snpeff/snpEff.jar" + makeWrapper ${jre}/bin/java $out/bin/snpsift --add-flags "-jar $out/libexec/snpeff/SnpSift.jar" + ''; + + meta = with stdenv.lib; { + description = "Genetic variant annotation and effect prediction toolbox."; + license = licenses.lgpl3; + homepage = http://snpeff.sourceforge.net/; + maintainers = with maintainers; [ jbedo ]; + platforms = platforms.all; + }; + +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index d59650440477..97c8741d6fa6 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -17008,6 +17008,8 @@ with pkgs; samtools = callPackage ../applications/science/biology/samtools/default.nix { }; + snpeff = callPackage ../applications/science/biology/snpeff/default.nix { }; + varscan = callPackage ../applications/science/biology/varscan/default.nix { }; bwa = callPackage ../applications/science/biology/bwa/default.nix { }; |