Merge commit '8746c77a383f5c76153c7a181f3616d273acfa2a'

6 files changed, 43 insertions, 13 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
index 406f42e9ad7b..2cdd7fda38ef 100644
--- a/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/bedtools/default.nix
@@ -1,17 +1,17 @@
-{stdenv, fetchFromGitHub, zlib, python}:
+{stdenv, fetchFromGitHub, zlib, python, bzip2, lzma}:
 
 stdenv.mkDerivation rec {
   name = "bedtools-${version}";
-  version = "2.27.1";
+  version = "2.28.0";
 
   src = fetchFromGitHub {
     owner = "arq5x";
     repo = "bedtools2";
     rev = "v${version}";
-    sha256 = "1pk68y052rm2m24yfmy82ms8p6kd6xcqxxgi7n0a1sbh89wllm6s";
+    sha256 = "1266bcn5hgbvysfi6nr4cqxlbxcx7vn7ng8kb0v3gz37qh2zxxw9";
   };
 
-  buildInputs = [ zlib python ];
+  buildInputs = [ zlib python bzip2 lzma ];
   cc = if stdenv.cc.isClang then "clang++" else "g++";
   buildPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} -j $NIX_BUILD_CORES";
   installPhase = "make prefix=$out SHELL=${stdenv.shell} CXX=${cc} install";
diff --git a/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix b/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix
new file mode 100644
index 000000000000..dcc725233551
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/est-sfs/default.nix
@@ -0,0 +1,28 @@
+{ stdenv, fetchurl, gsl }:
+
+stdenv.mkDerivation rec {
+  pname = "est-sfs";
+  version = "2.03";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/est-usfs/${pname}-release-${version}.tar.gz";
+    sha256 = "1hvamrgagz0xi89w8qafyd9mjrdpyika8zm22drddnjkp4sdj65n";
+  };
+
+  buildInputs = [ gsl ];
+
+  installPhase = ''
+    mkdir -p $out/bin
+    mkdir -p $out/share/doc/${pname}
+    cp est-sfs $out/bin
+    cp est-sfs-documentation.pdf $out/share/doc/${pname}
+  '';
+
+  meta = with stdenv.lib; {
+    homepage = https://sourceforge.net/projects/est-usfs;
+    description = "Estimate the unfolded site frequency spectrum and ancestral states";
+    license = licenses.gpl3;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.all;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix b/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
index 9ccf54a81133..9d41fed06911 100644
--- a/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/hisat2/default.nix
@@ -1,4 +1,4 @@
-{stdenv, fetchurl, unzip, which, python}:
+{stdenv, fetchurl, unzip, which, python, perl}:
 
 stdenv.mkDerivation rec {
   name = "hisat2-${version}";
@@ -9,7 +9,8 @@ stdenv.mkDerivation rec {
     sha256 = "10g73sdf6vqqfhhd92hliw7bbpkb8v4pp5012r5l21zws7p7d8l9";
   };
 
-  buildInputs = [ unzip  which python ];
+  nativeBuildInputs = [ unzip which ];
+  buildInputs = [ python perl ];
 
   installPhase = ''
     mkdir -p $out/bin
diff --git a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
index 5fc222bb2993..70c72779c52a 100644
--- a/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/picard-tools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   name = "picard-tools-${version}";
-  version = "2.20.2";
+  version = "2.20.4";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "0qpc6pi3fmzv8rs5cmk3dd4clrkzbrngsl384b5g0y7471lhavbi";
+    sha256 = "1z2zpwqhk8i7l9awajdrzxwij0vcmkwq7rajzjil7n65apj2hz9i";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
index d188ca02b183..e778c3bd52cc 100644
--- a/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/stacks/default.nix
@@ -2,10 +2,10 @@
     
 stdenv.mkDerivation rec {
   pname = "stacks";
-  version = "2.4";
+  version = "2.41";
   src = fetchurl {
     url = "http://catchenlab.life.illinois.edu/stacks/source/${pname}-${version}.tar.gz";
-    sha256 = "1ha1avkh6rqqvsy4k42336a2gj14y1jq19a2x8cjmiidi9l3s29h";
+    sha256 = "0q420rzjb05jfchcls3pysm4hxfgs6xj2jw246isx0il10g93gkq";
   };
 
   buildInputs = [ zlib ];
diff --git a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix
index 1527f5d3ddad..e7f5eab8bfaf 100644
--- a/nixpkgs/pkgs/applications/science/biology/strelka/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/strelka/default.nix
@@ -2,16 +2,17 @@
 
 stdenv.mkDerivation rec {
   name = "strelka-${version}";
-  version = "2.9.5";
+  version = "2.9.10";
 
   src = fetchFromGitHub {
     owner = "Illumina";
     repo = "strelka";
     rev = "v${version}";
-    sha256 = "0x4a6nkx1jnyag9svghsdjz1fz6q7qx5pn77wphdfnk81f9yspf8";
+    sha256 = "1nykbmim1124xh22nrhrsn8xgjb3s2y7akrdapn9sl1gdych4ppf";
   };
 
-  buildInputs = [ cmake zlib python2 ];
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib python2 ];
 
   preConfigure = ''
     sed -i 's|/usr/bin/env python|${python2}/bin/python|' src/python/lib/makeRunScript.py