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{stdenv, fetchurl, unzip, which, python, perl}:
stdenv.mkDerivation rec {
pname = "hisat2";
version = "2.1.0";
src = fetchurl {
url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-${version}-source.zip";
sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
};
nativeBuildInputs = [ unzip which ];
buildInputs = [ python 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 \
hisatgenotype_build_genome.py \
hisatgenotype_extract_reads.py \
hisatgenotype_extract_vars.py \
hisatgenotype_hla_cyp.py \
hisatgenotype_locus.py \
hisatgenotype.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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