47 lines
1.9 KiB
Nix
47 lines
1.9 KiB
Nix
{ lib, stdenv, fetchzip, jre, makeWrapper, python3 }:
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stdenv.mkDerivation rec {
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pname = "gatk";
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version = "4.3.0.0";
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src = fetchzip {
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url = "https://github.com/broadinstitute/gatk/releases/download/${version}/gatk-${version}.zip";
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sha256 = "sha256-AhXZyWbAXM5iwqxkYkMlqYUN838BjvIf5X95MVEfJ2I=";
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};
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nativeBuildInputs = [ makeWrapper ];
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buildInputs = [ python3 ];
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dontUnpack = true;
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installPhase = ''
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mkdir -p $out/bin
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install -m755 -D $src/gatk-package-${version}-local.jar $out/bin/
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install -m755 -D $src/gatk-package-${version}-spark.jar $out/bin/
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install -m755 -D $src/gatk $out/bin/
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'';
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postFixup = ''
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wrapProgram $out/bin/gatk --prefix PATH : ${lib.makeBinPath [ jre ]}
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'';
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meta = with lib; {
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homepage = "https://gatk.broadinstitute.org/hc/en-us";
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description = "A wide variety of tools with a primary focus on variant discovery and genotyping." ;
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license = licenses.asl20;
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sourceProvenance = with lib.sourceTypes; [ binaryBytecode ] ;
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maintainers = with maintainers; [ apraga ];
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longDescription = ''
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The GATK is the industry standard for identifying SNPs and indels in germline
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DNA and RNAseq data. Its scope is now expanding to include somatic short variant
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calling, and to tackle copy number (CNV) and structural variation (SV). In
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addition to the variant callers themselves, the GATK also includes many
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utilities to perform related tasks such as processing and quality control of
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high-throughput sequencing data, and bundles the popular Picard toolkit.
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These tools were primarily designed to process exomes and whole genomes
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generated with Illumina sequencing technology, but they can be adapted to handle
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a variety of other technologies and experimental designs. And although it was
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originally developed for human genetics, the GATK has since evolved to handle
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genome data from any organism, with any level of ploidy.
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'';
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};
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}
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