3 files changed, 39 insertions, 4 deletions
diff --git a/pkgs/applications/science/biology/manta/default.nix b/pkgs/applications/science/biology/manta/default.nix
new file mode 100644
index 00000000000..f0f0575e055
--- /dev/null
+++ b/pkgs/applications/science/biology/manta/default.nix
@@ -0,0 +1,35 @@
+{ stdenv, fetchFromGitHub, cmake, zlib, python2 }:
+
+stdenv.mkDerivation rec {
+  pname = "manta";
+  version = "1.6.0";
+
+  src = fetchFromGitHub {
+    owner = "Illumina";
+    repo = "manta";
+    rev = "v${version}";
+    sha256 = "1711xkcw8rpw9xv3bbm7v1aryjz4r341rkq5255192dg38sgq7w2";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ zlib python2 ];
+  postFixup = ''
+    sed -i 's|/usr/bin/env python2|${python2.interpreter}|' $out/lib/python/makeRunScript.py
+    sed -i 's|/usr/bin/env python|${python2.interpreter}|' $out/lib/python/pyflow/pyflow.py
+    sed -i 's|/bin/bash|${stdenv.shell}|' $out/lib/python/pyflow/pyflowTaskWrapper.py
+  '';
+  doInstallCheck = true;
+  installCheckPhase = ''
+    rm $out/lib/python/**/*.pyc
+    PYTHONPATH=$out/lib/python:$PYTHONPATH python -c 'import makeRunScript'
+    PYTHONPATH=$out/lib/python/pyflow:$PYTHONPATH python -c 'import pyflowTaskWrapper; import pyflow'
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Structural variant caller";
+    license = licenses.gpl3;
+    homepage = "https://github.com/Illumina/manta";
+    maintainers = with maintainers; [ jbedo ];
+    platforms =  platforms.x86_64;
+  };
+}
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index a67653c8437..44247f294aa 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 {
   pname = "picard-tools";
-  version = "2.21.3";
+  version = "2.21.6";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "0s1gn2bkya41866kd8zj0g8xjbivs763jqmlzdpjz4c25h6xkhns";
+    sha256 = "1vpyzhrs3bbviwk2n7k5296rnsw7g9ksvjsibl0gm7dawip9jb5s";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/applications/science/biology/samtools/default.nix b/pkgs/applications/science/biology/samtools/default.nix
index daa2925de7c..f2c5e9f25be 100644
--- a/pkgs/applications/science/biology/samtools/default.nix
+++ b/pkgs/applications/science/biology/samtools/default.nix
@@ -2,11 +2,11 @@
 
 stdenv.mkDerivation rec {
   pname = "samtools";
-  version = "1.9";
+  version = "1.10";
 
   src = fetchurl {
     url = "https://github.com/samtools/samtools/releases/download/${version}/${pname}-${version}.tar.bz2";
-    sha256 = "10ilqbmm7ri8z431sn90lvbjwizd0hhkf9rcqw8j823hf26nhgq8";
+    sha256 = "119ms0dpydw8dkh3zc4yyw9zhdzgv12px4l2kayigv31bpqcb7kv";
   };
 
   nativeBuildInputs = [ perl ];