Merge commit 'd26027792812fbfad4d0f451b5f47fdabf7fdeb9'

5 files changed, 68 insertions, 7 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/ants/default.nix b/nixpkgs/pkgs/applications/science/biology/ants/default.nix
index f54bd9af0288..d1a990a5eb28 100644
--- a/nixpkgs/pkgs/applications/science/biology/ants/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/ants/default.nix
@@ -15,9 +15,7 @@ stdenv.mkDerivation rec {
   nativeBuildInputs = [ cmake makeWrapper ];
   buildInputs = [ itk vtk ];
 
-  cmakeFlags = [ "-DANTS_SUPERBUILD=FALSE" "-DUSE_VTK=TRUE"
-                 # as cmake otherwise tries to download test data:
-                 "-DBUILD_TESTING=FALSE" ];
+  cmakeFlags = [ "-DANTS_SUPERBUILD=FALSE" "-DUSE_VTK=TRUE" ];
 
   enableParallelBuilding = true;
 
diff --git a/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix b/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix
new file mode 100644
index 000000000000..a15425ec2137
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/eggnog-mapper/default.nix
@@ -0,0 +1,40 @@
+{ stdenv, fetchFromGitHub, fetchpatch, makeWrapper, python27Packages, wget, diamond, hmmer }:
+
+python27Packages.buildPythonApplication rec {
+  pname = "eggnog-mapper";
+  version = "1.0.3";
+
+  src = fetchFromGitHub {
+    owner = "eggnogdb";
+    repo = "eggnog-mapper";
+    rev = "${version}";
+    sha256 = "1aaaflppy84bhkh2hb5gnzm4xgrz0rz0cgfpadr9w8cva8p0sqdv";
+  };
+
+  patches = (fetchpatch {
+    url = https://github.com/eggnogdb/eggnog-mapper/pull/125/commits/b7828e4c8c1c453e391aef050f06ff3f84ff9faf.patch;
+    sha256 = "0nz1a7ybm4j5c7vdm3annnxz9036iam2044hia341a0am9wydmzk";
+  });
+
+  buildInputs = [ makeWrapper ];
+  propagatedBuildInputs = [ python27Packages.biopython wget diamond hmmer ];
+
+  # make emapper find diamond & hmmer
+  makeWrapperArgs = [
+    ''--prefix PATH ':' "${diamond}/bin"''
+    ''--prefix PATH ':' "${hmmer}/bin"''
+    ];
+
+  # Tests rely on some of the databases being available, which is not bundled
+  # with this package as (1) in total, they represent >100GB of data, and (2)
+  # the user can download only those that interest them.
+  doCheck = false;
+
+  meta = with stdenv.lib; {
+    description = "Fast genome-wide functional annotation through orthology assignment";
+    license = licenses.gpl2;
+    homepage = https://github.com/eggnogdb/eggnog-mapper/wiki;
+    maintainers = with maintainers; [ luispedro ];
+    platforms = platforms.all;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/migrate/default.nix b/nixpkgs/pkgs/applications/science/biology/migrate/default.nix
new file mode 100644
index 000000000000..d80e6e7b30df
--- /dev/null
+++ b/nixpkgs/pkgs/applications/science/biology/migrate/default.nix
@@ -0,0 +1,24 @@
+{ gccStdenv, fetchurl, zlib, openmpi }:
+
+gccStdenv.mkDerivation rec {
+  version = "3.7.2";
+  pname = "migrate";
+
+  src = fetchurl {
+    url = "https://peterbeerli.com/migrate-html5/download_version3/${pname}-${version}.src.tar.gz";
+    sha256 = "1p2364ffjc56i82snzvjpy6pkf6wvqwvlvlqxliscx2c303fxs8v";
+  };
+
+  buildInputs = [ zlib openmpi ];
+  setSourceRoot = ''sourceRoot=$(echo */src)'';
+  buildFlags = [ "thread" "mpis" ];
+  preInstall = "mkdir -p $out/man/man1";
+
+  meta = with gccStdenv.lib; {
+    description = "Estimates population size, migration, population splitting parameters using genetic/genomic data";
+    homepage = https://peterbeerli.com/migrate-html5/index.html;
+    license = licenses.mit;
+    maintainers = [ maintainers.bzizou ];
+    platforms = platforms.unix;
+  };
+}
diff --git a/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix b/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix
index 5901b696d642..ab22fb7232ff 100644
--- a/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/mni_autoreg/default.nix
@@ -15,7 +15,7 @@ stdenv.mkDerivation rec {
   buildInputs = [ libminc ];
   propagatedBuildInputs = with perlPackages; [ perl GetoptTabular MNI-Perllib ];
 
-  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" "-DBUILD_TESTING=FALSE" ];
+  cmakeFlags = [ "-DLIBMINC_DIR=${libminc}/lib/" ];
   # testing broken: './minc_wrapper: Permission denied' from Testing/ellipse0.mnc
 
   postFixup = ''
@@ -33,4 +33,3 @@ stdenv.mkDerivation rec {
     license = licenses.free;
   };
 }
-
diff --git a/nixpkgs/pkgs/applications/science/biology/star/default.nix b/nixpkgs/pkgs/applications/science/biology/star/default.nix
index eb62a8c331f8..2f21da02fb00 100644
--- a/nixpkgs/pkgs/applications/science/biology/star/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/star/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   name = "star-${version}";
-  version = "2.7.0c";
+  version = "2.7.0f";
 
   src = fetchFromGitHub {
     repo = "STAR";
     owner = "alexdobin";
     rev = version;
-    sha256 = "0r5jcckr45f71jwhz8xazi1w6kfhszq3y6r7f6zl9963ms1q1gfv";
+    sha256 = "0ndqlyimf7xf00nghn8awg12pw985ixghiypg98r2gdm7pscgd0i";
   };
 
   sourceRoot = "source/source";