8 files changed, 53 insertions, 9 deletions
diff --git a/pkgs/applications/science/biology/ants/default.nix b/pkgs/applications/science/biology/ants/default.nix
index 20eedfaaa16..cb88e92fe1c 100644
--- a/pkgs/applications/science/biology/ants/default.nix
+++ b/pkgs/applications/science/biology/ants/default.nix
@@ -1,4 +1,4 @@
-{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk }:
+{ stdenv, fetchFromGitHub, fetchpatch, cmake, makeWrapper, itk4, vtk_7 }:
 
 stdenv.mkDerivation rec {
   pname    = "ANTs";
@@ -20,7 +20,7 @@ stdenv.mkDerivation rec {
   ];
 
   nativeBuildInputs = [ cmake makeWrapper ];
-  buildInputs = [ itk4 vtk ];
+  buildInputs = [ itk4 vtk_7 ];
 
   cmakeFlags = [ "-DANTS_SUPERBUILD=FALSE" "-DUSE_VTK=TRUE" ];
 
diff --git a/pkgs/applications/science/biology/bppsuite/default.nix b/pkgs/applications/science/biology/bppsuite/default.nix
new file mode 100644
index 00000000000..564a38708bc
--- /dev/null
+++ b/pkgs/applications/science/biology/bppsuite/default.nix
@@ -0,0 +1,21 @@
+{ stdenv, fetchFromGitHub, cmake, bpp-core, bpp-seq, bpp-phyl, bpp-popgen }:
+
+stdenv.mkDerivation rec {
+  pname = "bppsuite";
+
+  inherit (bpp-core) version;
+
+  src = fetchFromGitHub {
+    owner = "BioPP";
+    repo = pname;
+    rev = "v${version}";
+    sha256 = "1wdwcgczqbc3m116vakvi0129wm3acln3cfc7ivqnalwvi6lrpds";
+  };
+
+  nativeBuildInputs = [ cmake ];
+  buildInputs = [ bpp-core bpp-seq bpp-phyl bpp-popgen ];
+
+  meta = bpp-core.meta // {
+    changelog = "https://github.com/BioPP/bppsuite/blob/master/ChangeLog";
+  };
+}
diff --git a/pkgs/applications/science/biology/picard-tools/default.nix b/pkgs/applications/science/biology/picard-tools/default.nix
index 1e678d4b6ed..4b455eaca6f 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 = "2.22.7";
+  version = "2.22.8";
 
   src = fetchurl {
     url = "https://github.com/broadinstitute/picard/releases/download/${version}/picard.jar";
-    sha256 = "09q66lhjnprkw8azavwzwv9dlhr9b4x0dbz6fym0i2wbhylqp4w6";
+    sha256 = "0g387jlf7r1p2kx8gya3vxksbjy3y2ywxa7yjqmxg3y8725fyixl";
   };
 
   nativeBuildInputs = [ makeWrapper ];
diff --git a/pkgs/applications/science/logic/lean/default.nix b/pkgs/applications/science/logic/lean/default.nix
index ed077b03908..2f5943dfa9b 100644
--- a/pkgs/applications/science/logic/lean/default.nix
+++ b/pkgs/applications/science/logic/lean/default.nix
@@ -2,13 +2,13 @@
 
 stdenv.mkDerivation rec {
   pname = "lean";
-  version = "3.13.1";
+  version = "3.14.0";
 
   src = fetchFromGitHub {
     owner  = "leanprover-community";
     repo   = "lean";
     rev    = "v${version}";
-    sha256 = "1ak5l40h5yjlbzz92l724l6bm5q341cg6k1yk13sbwn42l8szsar";
+    sha256 = "1dlzap3j26rh93ick1lqb7g3jkqjpd33gl4gqfcbx22v62258y5b";
   };
 
   nativeBuildInputs = [ cmake ];
diff --git a/pkgs/applications/science/logic/sad/default.nix b/pkgs/applications/science/logic/sad/default.nix
index f9b82b5d733..f1066abf693 100644
--- a/pkgs/applications/science/logic/sad/default.nix
+++ b/pkgs/applications/science/logic/sad/default.nix
@@ -8,7 +8,7 @@ stdenv.mkDerivation {
   };
   buildInputs = [ haskell.compiler.ghc844 spass ];
   patches = [
-    ./patch
+    ./patch.patch
     # Since the LTS 12.0 update, <> is an operator in Prelude, colliding with
     # the <> operator with a different meaning defined by this package
     ./monoid.patch
diff --git a/pkgs/applications/science/logic/sad/patch b/pkgs/applications/science/logic/sad/patch.patch
index a5b1d617708..a5b1d617708 100644
--- a/pkgs/applications/science/logic/sad/patch
+++ b/pkgs/applications/science/logic/sad/patch.patch
diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
index 741330e4ad2..63a727f9c88 100644
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@@ -2,7 +2,7 @@
 
 python3Packages.buildPythonApplication rec {
   pname = "snakemake";
-  version = "5.16.0";
+  version = "5.17.0";
 
   propagatedBuildInputs = with python3Packages; [
     appdirs
@@ -22,7 +22,7 @@ python3Packages.buildPythonApplication rec {
 
   src = python3Packages.fetchPypi {
     inherit pname version;
-    sha256 = "0jlf3y8b1gdv5xz37yk9b5g2b65zkk45p15x0ypvd2blpzy80537";
+    sha256 = "0y652i3saqq2z61yvk0i6q3lnq2xfrygcxms5gygspj71q2n4f7k";
   };
 
   doCheck = false; # Tests depend on Google Cloud credentials at ${HOME}/gcloud-service-key.json
diff --git a/pkgs/applications/science/physics/xflr5/default.nix b/pkgs/applications/science/physics/xflr5/default.nix
new file mode 100644
index 00000000000..85838b04cbf
--- /dev/null
+++ b/pkgs/applications/science/physics/xflr5/default.nix
@@ -0,0 +1,23 @@
+{ stdenv, lib, fetchurl, wrapQtAppsHook, qmake }:
+
+stdenv.mkDerivation rec {
+  pname = "xflr5";
+  version = "6.47";
+
+  src = fetchurl {
+    url = "mirror://sourceforge/xflr5/${pname}_v${version}_src.tar.gz";
+    sha256 = "02x3r9iv3ndwxa65mxn9m5dlhcrnjiq7cffi6rmb456gs3v3dnav";
+  };
+
+  enableParallelBuilding = true;
+
+  nativeBuildInputs = [ qmake wrapQtAppsHook ];
+
+  meta = with stdenv.lib; {
+    description = "An analysis tool for airfoils, wings and planes";
+    homepage = https://sourceforge.net/projects/xflr5/;
+    license = licenses.gpl3;
+    maintainers = [ maintainers.esclear ];
+    platforms = platforms.linux;
+  };
+}
\ No newline at end of file