diff --git a/pkgs/applications/misc/mysql-workbench/dont-search-for-antlr-jar.patch b/pkgs/by-name/my/mysql-workbench/dont-search-for-antlr-jar.patch
similarity index 100%
rename from pkgs/applications/misc/mysql-workbench/dont-search-for-antlr-jar.patch
rename to pkgs/by-name/my/mysql-workbench/dont-search-for-antlr-jar.patch
diff --git a/pkgs/applications/misc/mysql-workbench/fix-swig-build.patch b/pkgs/by-name/my/mysql-workbench/fix-swig-build.patch
similarity index 100%
rename from pkgs/applications/misc/mysql-workbench/fix-swig-build.patch
rename to pkgs/by-name/my/mysql-workbench/fix-swig-build.patch
diff --git a/pkgs/applications/misc/mysql-workbench/hardcode-paths.patch b/pkgs/by-name/my/mysql-workbench/hardcode-paths.patch
similarity index 100%
rename from pkgs/applications/misc/mysql-workbench/hardcode-paths.patch
rename to pkgs/by-name/my/mysql-workbench/hardcode-paths.patch
diff --git a/pkgs/applications/misc/mysql-workbench/default.nix b/pkgs/by-name/my/mysql-workbench/package.nix
similarity index 74%
rename from pkgs/applications/misc/mysql-workbench/default.nix
rename to pkgs/by-name/my/mysql-workbench/package.nix
index bc33c7259c45..9828074955f2 100644
--- a/pkgs/applications/misc/mysql-workbench/default.nix
+++ b/pkgs/by-name/my/mysql-workbench/package.nix
@@ -3,49 +3,52 @@
   stdenv,
   fetchurl,
   replaceVars,
+
   cmake,
   ninja,
   pkg-config,
-  glibc,
-  gtk3,
-  gtkmm3,
-  pcre,
+  jre,
   swig,
-  antlr4_12,
+  wrapGAppsHook3,
+
+  bash,
+  coreutils,
+  glibc,
   sudo,
+
+  cairo,
   mysql,
+  libiodbc,
+  proj,
+
+  antlr4_12,
+  gtkmm3,
   libxml2,
   libmysqlconnectorcpp,
   vsqlite,
   gdal,
-  libiodbc,
-  libpthreadstubs,
-  libXdmcp,
+  boost,
+  libssh,
+  openssl,
+  rapidjson,
   libuuid,
   libzip,
   libsecret,
-  libssh,
-  python3,
-  jre,
-  boost,
-  libsigcxx,
-  libX11,
-  openssl,
-  rapidjson,
-  proj,
-  cairo,
-  libxkbcommon,
-  libepoxy,
-  wrapGAppsHook3,
-  at-spi2-core,
-  dbus,
-  bash,
-  coreutils,
-  zstd,
+  python3Packages,
 }:
 
 let
-  inherit (python3.pkgs) paramiko pycairo pyodbc;
+  # for some reason the package doesn't build with swig 4.3.0
+  swig_4_2 = swig.overrideAttrs (prevAttrs: {
+    version = "4.2.1";
+    src = prevAttrs.src.override {
+      hash = "sha256-VlUsiRZLScmbC7hZDzKqUr9481YXVwo0eXT/jy6Fda8=";
+    };
+  });
+
+  getCoreExe = lib.getExe' coreutils;
+
+  inherit (python3Packages) paramiko pycairo pyodbc;
 in
 stdenv.mkDerivation (finalAttrs: {
   pname = "mysql-workbench";
@@ -58,23 +61,23 @@ stdenv.mkDerivation (finalAttrs: {
 
   patches = [
     (replaceVars ./hardcode-paths.patch {
-      catchsegv = "${glibc.bin}/bin/catchsegv";
-      bash = "${bash}/bin/bash";
-      cp = "${coreutils}/bin/cp";
-      dd = "${coreutils}/bin/dd";
-      ls = "${coreutils}/bin/ls";
-      mkdir = "${coreutils}/bin/mkdir";
-      nohup = "${coreutils}/bin/nohup";
-      rm = "${coreutils}/bin/rm";
-      rmdir = "${coreutils}/bin/rmdir";
-      stat = "${coreutils}/bin/stat";
-      sudo = "${sudo}/bin/sudo";
+      bash = lib.getExe bash;
+      catchsegv = lib.getExe' glibc "catchsegv";
+      cp = getCoreExe "cp";
+      dd = getCoreExe "dd";
+      ls = getCoreExe "ls";
+      mkdir = getCoreExe "mkdir";
+      nohup = getCoreExe "nohup";
+      rm = getCoreExe "rm";
+      rmdir = getCoreExe "rmdir";
+      stat = getCoreExe "stat";
+      sudo = lib.getExe sudo;
     })
 
     # Fix swig not being able to find headers
     # https://github.com/NixOS/nixpkgs/pull/82362#issuecomment-597948461
     (replaceVars ./fix-swig-build.patch {
-      cairoDev = "${cairo.dev}";
+      cairoDev = lib.getDev cairo;
     })
 
     # Don't try to override the ANTLR_JAR_PATH specified in cmakeFlags
@@ -93,17 +96,13 @@ stdenv.mkDerivation (finalAttrs: {
     ninja
     pkg-config
     jre
-    swig
+    swig_4_2
     wrapGAppsHook3
   ];
 
   buildInputs = [
-    gtk3
-    gtkmm3
-    libX11
     antlr4_12.runtime.cpp
-    python3
-    mysql
+    gtkmm3
     (libxml2.override { enableHttp = true; })
     libmysqlconnectorcpp
     vsqlite
@@ -112,29 +111,16 @@ stdenv.mkDerivation (finalAttrs: {
     libssh
     openssl
     rapidjson
-    libiodbc
-    pcre
-    cairo
     libuuid
     libzip
     libsecret
-    libsigcxx
-    proj
+    libiodbc
 
     # python dependencies:
     paramiko
     pycairo
     pyodbc
     # TODO: package sqlanydb and add it here
-
-    # transitive dependencies:
-    libpthreadstubs
-    libXdmcp
-    libxkbcommon
-    libepoxy
-    at-spi2-core
-    dbus
-    zstd
   ];
 
   env.NIX_CFLAGS_COMPILE = toString (
@@ -153,13 +139,13 @@ stdenv.mkDerivation (finalAttrs: {
   );
 
   cmakeFlags = [
-    "-DMySQL_CONFIG_PATH=${mysql}/bin/mysql_config"
-    "-DIODBC_CONFIG_PATH=${libiodbc}/bin/iodbc-config"
+    (lib.cmakeFeature "MySQL_CONFIG_PATH" (lib.getExe' mysql "mysql_config"))
+    (lib.cmakeFeature "IODBC_CONFIG_PATH" (lib.getExe' libiodbc "iodbc-config"))
+    (lib.cmakeFeature "ANTLR_JAR_PATH" "${antlr4_12.jarLocation}")
     # mysql-workbench 8.0.21 depends on libmysqlconnectorcpp 1.1.8.
     # Newer versions of connector still provide the legacy library when enabled
     # but the headers are in a different location.
-    "-DANTLR_JAR_PATH=${antlr4_12.jarLocation}"
-    "-DMySQLCppConn_INCLUDE_DIR=${libmysqlconnectorcpp}/include/jdbc"
+    (lib.cmakeFeature "MySQLCppConn_INCLUDE_DIR" "${lib.getDev libmysqlconnectorcpp}/include/jdbc")
   ];
 
   # There is already an executable and a wrapper in bindir
@@ -168,8 +154,8 @@ stdenv.mkDerivation (finalAttrs: {
 
   preFixup = ''
     gappsWrapperArgs+=(
-      --prefix PATH : "${python3}/bin"
-      --prefix PROJSO : "${proj}/lib/libproj.so"
+      --prefix PATH : "${lib.makeBinPath [ python3Packages.python ]}"
+      --prefix PROJSO : "${lib.getLib proj}/lib/libproj.so"
       --set PYTHONPATH $PYTHONPATH
     )
   '';
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f2036862232f..d65e0026d344 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -18148,12 +18148,11 @@ with pkgs;
 
   lice = python3Packages.callPackage ../tools/misc/lice { };
 
-  mysql-workbench = callPackage ../applications/misc/mysql-workbench (let mysql = mysql80; in {
+  mysql-workbench = callPackage ../by-name/my/mysql-workbench/package.nix (let mysql = mysql80; in {
     gdal = gdal.override {
       libmysqlclient = mysql;
     };
     mysql = mysql;
-    pcre = pcre-cpp;
   });
 
   resp-app = libsForQt5.callPackage ../applications/misc/resp-app { };