Merge commit 'beff2f8d75ef2c65017fb25e251337c6bb2e950d'

v#	modified:   nixpkgs/pkgs/tools/networking/dhcpcd/default.nix

3 files changed, 40 insertions, 9 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
index 781ceb3df59e..0e2b5d8b25fe 100644
--- a/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/dcm2niix/default.nix
@@ -2,21 +2,22 @@
 , fetchFromGitHub
 , cmake
 , libyamlcpp
+, git
 }:
 
 stdenv.mkDerivation rec {
-  version = "1.0.20170130";
+  version = "1.0.20190410";
   name = "dcm2niix-${version}";
 
   src = fetchFromGitHub {
     owner = "rordenlab";
     repo = "dcm2niix";
     rev = "v${version}";
-    sha256 = "1f2nzd8flp1rfn725bi64z7aw3ccxyyygzarxijw6pvgl476i532";
+    sha256 = "1prwpvbi76xlpkhc4kadjhyyx0s71cs30hi6anknhfm6hdyd26ms";
   };
 
   enableParallelBuilding = true;
-  nativeBuildInputs = [ cmake ];
+  nativeBuildInputs = [ cmake git ];
   buildInputs = [ libyamlcpp ];
 
   meta = with stdenv.lib; {
diff --git a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
index 3cd83a5cdd27..1bdb31616e4d 100644
--- a/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/mosdepth/default.nix
@@ -4,26 +4,26 @@ let
   hts-nim = fetchFromGitHub {
     owner = "brentp";
     repo = "hts-nim";
-    rev = "v0.2.5";
-    sha256 = "1fma99rjqxgg9dihkd10hm1jjp5amsk5wsxnvq1lk4mcsjix5xqb";
+    rev = "v0.2.14";
+    sha256 = "0d1z4b6mrppmz3hgkxd4wcy79w68icvhi7q7n3m2k17n8f3xbdx3";
   };
 
   docopt = fetchFromGitHub {
     owner = "docopt";
     repo = "docopt.nim";
-    rev = "v0.6.5";
-    sha256 = "0yx79m4jkdcazwlky55nwf39zj5kdhymrrdrjq29mahiwx83x5zr";
+    rev = "v0.6.7";
+    sha256 = "1ga7ckg21fzwwvh26jp2phn2h3pvkn8g8sm13dxif33rp471bv37";
   };
 
 in stdenv.mkDerivation rec {
   name = "mosdepth-${version}";
-  version = "0.2.3";
+  version = "0.2.6";
 
   src = fetchFromGitHub {
     owner = "brentp";
     repo = "mosdepth";
     rev = "v${version}";
-    sha256 = "1b9frrwhcvay3alhn0d02jccc2qlbij1732hzq9nhwnr4kvsvxx7";
+    sha256 = "0i9pl9lsli3y84ygxanrr525gfg8fs9h481944cbzsmqmbldwvgk";
   };
 
   buildInputs = [ nim ];
diff --git a/nixpkgs/pkgs/applications/science/biology/octopus/default.nix b/nixpkgs/pkgs/applications/science/biology/octopus/default.nix
new file mode 100644
index 000000000000..0a2074a06e97
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/octopus/default.nix
@@ -0,0 +1,30 @@
+{stdenv, fetchFromGitHub, cmake, boost, gmp, htslib, zlib, lzma, pkg-config}:
+
+stdenv.mkDerivation rec {
+  pname = "octopus";
+  version = "0.6.3-beta";
+  name = "${pname}-${version}";
+
+  src = fetchFromGitHub {
+    owner = "luntergroup";
+    repo = "octopus";
+    rev = "v${version}";
+    sha256 = "042fycg8ppld7iajpzq2d8h8wr0nw43zbl57y125sfihryvr373n";
+  };
+
+  nativeBuildInputs = [ cmake pkg-config ];
+  buildInputs = [ boost gmp htslib zlib lzma ];
+
+  postInstall = ''
+    mkdir $out/bin
+    mv $out/octopus $out/bin
+  '';
+
+  meta = with stdenv.lib; {
+    description = "Bayesian haplotype-based mutation calling";
+    license = licenses.mit;
+    homepage = "https://github.com/luntergroup/octopus";
+    maintainers = with maintainers; [ jbedo ];
+    platforms = platforms.x86_64;
+  };
+}