diff options
Diffstat (limited to 'nixpkgs/pkgs/applications/science/biology')
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 ]; |