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Merge pull request #45102 from jbedo/hisat2

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hisat2: init 2.1.0
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Matthew Bauer 2018-09-10 15:11:58 -05:00 committed by GitHub
commit 40d19d8e7c
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49
pkgs/applications/science/biology/hisat2/default.nix Normal file
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@ -0,0 +1,49 @@
{stdenv, fetchurl, unzip, which, python}:
stdenv.mkDerivation rec {
name = "hisat2-${version}";
version = "2.1.0";
src = fetchurl {
url = "ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-${version}-source.zip";
sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
};
buildInputs = [ unzip which python ];
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" ];
};
}

2
pkgs/top-level/all-packages.nix
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@ -20641,6 +20641,8 @@ with pkgs;
ezminc = callPackage ../applications/science/biology/EZminc { };
hisat2 = callPackage ../applications/science/biology/hisat2 { };
htslib = callPackage ../development/libraries/science/biology/htslib { };
igv = callPackage ../applications/science/biology/igv { };