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{stdenv, fetchFromGitHub, unzip, which, python3, perl}:
stdenv.mkDerivation rec {
pname = "hisat2";
version = "2.2.1";
src = fetchFromGitHub {
owner = "DaehwanKimLab";
repo = "hisat2";
rev = "v${version}";
sha256 = "0lmzdhzjkvxw7n5w40pbv5fgzd4cz0f9pxczswn3d4cr0k10k754";
};
nativeBuildInputs = [ unzip which ];
buildInputs = [ python3 perl ];
installPhase = ''
mkdir -p $out/bin
cp hisat2 \
hisat2-inspect-l \
hisat2-build-s \
hisat2-align-l \
hisat2-inspect \
hisat2-align-s \
hisat2-inspect-s \
hisat2-build-l \
hisat2-build \
extract_exons.py \
extract_splice_sites.py \
hisat2_extract_exons.py \
hisat2_extract_snps_haplotypes_UCSC.py \
hisat2_extract_snps_haplotypes_VCF.py \
hisat2_extract_splice_sites.py \
hisat2_simulate_reads.py \
$out/bin
'';
meta = with stdenv.lib; {
description = "Graph based aligner";
license = licenses.gpl3;
homepage = "https://ccb.jhu.edu/software/hisat2/index.shtml";
maintainers = with maintainers; [ jbedo ];
platforms = [ "x86_64-linux" "i686-linux" ];
};
}
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