3 files changed, 4 insertions, 36 deletions
diff --git a/pkgs/applications/science/biology/kent/default.nix b/pkgs/applications/science/biology/kent/default.nix
index 400e073f69057..56cfa5168a486 100644
--- a/pkgs/applications/science/biology/kent/default.nix
+++ b/pkgs/applications/science/biology/kent/default.nix
@@ -13,13 +13,13 @@
 }:
 stdenv.mkDerivation rec {
   pname = "kent";
-  version = "465";
+  version = "466";
 
   src = fetchFromGitHub {
     owner = "ucscGenomeBrowser";
     repo = pname;
     rev = "v${version}_base";
-    hash = "sha256-QeHqXSbad5LCmQ8DfLxl2pyXJvKV4G7uLXBtRd7LME0=";
+    hash = "sha256-zoDZ+8G0SHKfWmkXBqp+WSjQXtmkcTIZjrjPhUIJw1c=";
   };
 
   buildInputs = [ libpng libuuid zlib bzip2 xz openssl curl libmysqlclient ];
diff --git a/pkgs/applications/science/biology/spades/default.nix b/pkgs/applications/science/biology/spades/default.nix
deleted file mode 100644
index 0b0491a71aaef..0000000000000
--- a/pkgs/applications/science/biology/spades/default.nix
+++ /dev/null
@@ -1,32 +0,0 @@
-{ lib, stdenv, fetchurl, zlib, bzip2, cmake, python3 }:
-
-stdenv.mkDerivation rec {
-  pname = "SPAdes";
-  version = "3.15.5";
-
-  src = fetchurl {
-    url = "http://cab.spbu.ru/files/release${version}/${pname}-${version}.tar.gz";
-    sha256 = "sha256-FVw2QNVx8uexmgUDHR/Q0ZvYLfeF04hw+5O9JBsSu/o=";
-  };
-
-  nativeBuildInputs = [ cmake ];
-
-  buildInputs = [ zlib bzip2 python3 ];
-
-  doCheck = true;
-
-  sourceRoot = "${pname}-${version}/src";
-
-  env.CXXFLAGS = toString [
-    # GCC 13: error: 'uint32_t' does not name a type
-    "-include cstdint"
-  ];
-
-  meta = with lib; {
-    description = "St. Petersburg genome assembler: assembly toolkit containing various assembly pipelines";
-    license = licenses.gpl2Only;
-    homepage = "http://cab.spbu.ru/software/spades/";
-    platforms = [ "x86_64-linux" "x86_64-darwin" ];
-    maintainers = [ maintainers.bzizou ];
-  };
-}
diff --git a/pkgs/applications/science/misc/snakemake/default.nix b/pkgs/applications/science/misc/snakemake/default.nix
index ade5239762518..7f0e70c642134 100644
--- a/pkgs/applications/science/misc/snakemake/default.nix
+++ b/pkgs/applications/science/misc/snakemake/default.nix
@@ -6,14 +6,14 @@
 
 python3.pkgs.buildPythonApplication rec {
   pname = "snakemake";
-  version = "8.13.0";
+  version = "8.14.0";
   format = "setuptools";
 
   src = fetchFromGitHub {
     owner = "snakemake";
     repo = pname;
     rev = "refs/tags/v${version}";
-    hash = "sha256-Xd8mZ8tsemJ53hAMED2biRyDlEw/gG/Hh1iZSwSB1vY=";
+    hash = "sha256-6oguN4u4OUDXpDsbueSBNwtWgLCaKmgq3w/d/MsMh7Y=";
     # https://github.com/python-versioneer/python-versioneer/issues/217
     postFetch = ''
       sed -i "$out"/snakemake/_version.py -e 's#git_refnames = ".*"#git_refnames = " (tag: v${version})"#'