3 files changed, 53 insertions, 4 deletions
diff --git a/pkgs/applications/science/biology/hisat2/default.nix b/pkgs/applications/science/biology/hisat2/default.nix
new file mode 100644
index 000000000000..9ccf54a81133
--- /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/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index 0ddbdab4c1b1..c141e6087bfc 100644
--- a/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.18.11";
+  version = "2.18.12";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "03wkyz3bjx3n8bwambhz9lr09271r1wxycmx4p7m2naqs4afxb89";
+    sha256 = "0r5w71fcji4j3xjdhip9jlvmqi66x52af8b7mfxp4nz6xxl9ilxm";
   };
 
   buildInputs = [ jre makeWrapper ];
diff --git a/pkgs/applications/science/biology/star/default.nix b/pkgs/applications/science/biology/star/default.nix
index f52df902db6a..c552d9f9de35 100644
--- a/pkgs/applications/science/biology/star/default.nix
+++ b/pkgs/applications/science/biology/star/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "star-${version}";
-  version = "2.6.0c";
+  version = "2.6.1a";
 
   src = fetchFromGitHub {
     repo = "STAR";
     owner = "alexdobin";
     rev = version;
-    sha256 = "04cj6jw8d9q6lk9c78wa4fky6jdlicf1d13plq7182h8vqiz8p59";
+    sha256 = "11zs32d96gpjldrylz3nr5r2qrshf0nmzh5nmcy4wrk7y5lz81xc";
   };
 
   sourceRoot = "source/source";