Merge commit '0cbe9f69c234a7700596e943bfae7ef27a31b735' into HEAD

3 files changed, 20 insertions, 8 deletions

diff --git a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix
index eaf0b5932726..a199e41d50aa 100644
--- a/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/deeptools/default.nix
@@ -2,15 +2,17 @@
 with python.pkgs;
 buildPythonApplication rec {
   pname = "deepTools";
-  version = "3.5.1";
+  version = "3.5.4";
 
   src = fetchFromGitHub {
     owner = "deeptools";
     repo = "deepTools";
     rev = version;
-    sha256 = "07v8vb2x4b0mgw0mvcj91vj1fqbcwizwsniysl2cvmv93gad8gbp";
+    sha256 = "sha256-A8YdlMptmJyxWW0EYLjXFIWjIO/mttEC7VYdlCe9MaI=";
   };
 
+  format = "pyproject";
+
   propagatedBuildInputs = [
     numpy
     numpydoc
@@ -21,9 +23,10 @@ buildPythonApplication rec {
     matplotlib
     plotly
     deeptoolsintervals
+    importlib-metadata
   ];
 
-  nativeCheckInputs = [ nose ];
+  nativeCheckInputs = [ pytest ];
 
   meta = with lib; {
     homepage = "https://deeptools.readthedocs.io/en/develop";
@@ -36,7 +39,7 @@ buildPythonApplication rec {
       publication-ready visualizations to identify enrichments and for functional
       annotations of the genome.
     '';
-    license = licenses.gpl3;
+    license = with licenses; [ mit bsd3 ];
     maintainers = with maintainers; [ scalavision ];
   };
 }
diff --git a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix
index 78f226350f60..febfde548fd7 100644
--- a/nixpkgs/pkgs/applications/science/biology/dssp/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/dssp/default.nix
@@ -3,6 +3,7 @@
 , cmake
 , eigen
 , fetchFromGitHub
+, fetchpatch
 , libcifpp
 , libmcfp
 , zlib
@@ -15,18 +16,26 @@ let
       inherit (oldAttrs.src) owner repo rev;
       hash = "sha256-Sj10j6HxUoUvQ66cd2B8CO7CVBRd7w9CTovxkwPDOvs=";
     };
+    patches = [
+      (fetchpatch {
+        # https://github.com/PDB-REDO/libcifpp/issues/51
+        name = "fix-build-on-darwin.patch";
+        url = "https://github.com/PDB-REDO/libcifpp/commit/641f06a7e7c0dc54af242b373820f2398f59e7ac.patch";
+        hash = "sha256-eWNfp9nA/+2J6xjZR6Tj+5OM3L5MxdfRi0nBzyaqvS0=";
+      })
+    ];
   });
 in
 
 stdenv.mkDerivation (finalAttrs: {
   pname = "dssp";
-  version = "4.4.3";
+  version = "4.4.4.1";
 
   src = fetchFromGitHub {
     owner = "PDB-REDO";
     repo = "dssp";
     rev = "refs/tags/v${finalAttrs.version}";
-    hash = "sha256-zPmRR7sxVNErwabLqA5CNMO4K1qHdmC9FBPjcx91KuM=";
+    hash = "sha256-sy6GBCnTGRD1YP00dKIolkr1RMboLGcd0f4kU8gCOnA=";
   };
 
   nativeBuildInputs = [
diff --git a/nixpkgs/pkgs/applications/science/biology/raxml/default.nix b/nixpkgs/pkgs/applications/science/biology/raxml/default.nix
index d02d47266297..0cc20b063503 100644
--- a/nixpkgs/pkgs/applications/science/biology/raxml/default.nix
+++ b/nixpkgs/pkgs/applications/science/biology/raxml/default.nix
@@ -6,13 +6,13 @@
 
 stdenv.mkDerivation rec {
   pname = "RAxML${lib.optionalString useMpi "-mpi"}";
-  version = "8.2.12";
+  version = "8.2.13";
 
   src = fetchFromGitHub {
     owner = "stamatak";
     repo = "standard-RAxML";
     rev = "v${version}";
-    sha256 = "1jqjzhch0rips0vp04prvb8vmc20c5pdmsqn8knadcf91yy859fh";
+    sha256 = "sha256-w+Eqi0GhVira1H6ZnMNeZGBMzDjiGT7JSFpQEVXONyk=";
   };
 
   buildInputs = lib.optionals useMpi [ mpi ];