1 files changed, 46 insertions, 0 deletions
diff --git a/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix b/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
new file mode 100644
index 000000000000..ab8e26f92a0d
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
@@ -0,0 +1,46 @@
+{lib, 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 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" ];
+  };
+
+}