646b892680
Some checks failed
Periodic Merges (6h) / master → staging-nixos (push) Failing after 12m50s
Periodic Merges (6h) / master → staging-next (push) Failing after 12m54s
Periodic Merges (24h) / merge-base(master,staging) → haskell-updates (push) Failing after 11m54s
Periodic Merges (6h) / staging-next → staging (push) Failing after 12m13s
Periodic Merges (24h) / staging-next-25.05 → staging-25.05 (push) Failing after 13m24s
Periodic Merges (24h) / release-25.05 → staging-next-25.05 (push) Failing after 14m28s
55 lines
2.0 KiB
Nix
55 lines
2.0 KiB
Nix
{
|
|
lib,
|
|
stdenv,
|
|
fetchzip,
|
|
jre,
|
|
makeWrapper,
|
|
python3,
|
|
}:
|
|
|
|
stdenv.mkDerivation rec {
|
|
pname = "gatk";
|
|
version = "4.6.2.0";
|
|
src = fetchzip {
|
|
url = "https://github.com/broadinstitute/gatk/releases/download/${version}/gatk-${version}.zip";
|
|
sha256 = "sha256-I2p7BLh4q0i8qn1fTbzsaKVnCkMrPIxEpBUjOxNxgxI=";
|
|
};
|
|
|
|
nativeBuildInputs = [ makeWrapper ];
|
|
buildInputs = [ python3 ];
|
|
|
|
dontUnpack = true;
|
|
|
|
installPhase = ''
|
|
mkdir -p $out/bin
|
|
install -m755 -D $src/gatk-package-${version}-local.jar $out/bin/
|
|
install -m755 -D $src/gatk-package-${version}-spark.jar $out/bin/
|
|
install -m755 -D $src/gatk $out/bin/
|
|
'';
|
|
postFixup = ''
|
|
wrapProgram $out/bin/gatk --prefix PATH : ${lib.makeBinPath [ jre ]}
|
|
'';
|
|
|
|
meta = with lib; {
|
|
homepage = "https://gatk.broadinstitute.org/hc/en-us";
|
|
description = "Wide variety of tools with a primary focus on variant discovery and genotyping";
|
|
license = licenses.asl20;
|
|
sourceProvenance = with lib.sourceTypes; [ binaryBytecode ];
|
|
maintainers = with maintainers; [ apraga ];
|
|
longDescription = ''
|
|
The GATK is the industry standard for identifying SNPs and indels in germline
|
|
DNA and RNAseq data. Its scope is now expanding to include somatic short variant
|
|
calling, and to tackle copy number (CNV) and structural variation (SV). In
|
|
addition to the variant callers themselves, the GATK also includes many
|
|
utilities to perform related tasks such as processing and quality control of
|
|
high-throughput sequencing data, and bundles the popular Picard toolkit.
|
|
|
|
These tools were primarily designed to process exomes and whole genomes
|
|
generated with Illumina sequencing technology, but they can be adapted to handle
|
|
a variety of other technologies and experimental designs. And although it was
|
|
originally developed for human genetics, the GATK has since evolved to handle
|
|
genome data from any organism, with any level of ploidy.
|
|
'';
|
|
};
|
|
}
|