From 9bd7a4f5208cfa92c0ae8cca1ae6f69f0f8f242d Mon Sep 17 00:00:00 2001 From: Justin Bedo Date: Thu, 16 Aug 2018 17:23:14 +1000 Subject: [PATCH] hisat2: init 2.1.0 --- .../science/biology/hisat2/default.nix | 49 +++++++++++++++++++ pkgs/top-level/all-packages.nix | 2 + 2 files changed, 51 insertions(+) create mode 100644 pkgs/applications/science/biology/hisat2/default.nix diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix new file mode 100644 index 00000000000..9ccf54a8113 --- /dev/null +++ b/pkgs/applications/science/biology/hisat2/default.nix @@ -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" ]; + }; + +} diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix index 2846bf49eb8..48eae4eb6c1 100644 --- a/pkgs/top-level/all-packages.nix +++ b/pkgs/top-level/all-packages.nix @@ -20377,6 +20377,8 @@ 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 { };