cytoscape: move to by-name

pkgs/applications/science/misc/cytoscape/default.nix pkgs/by-name/cy/cytoscape/package.nix

···
   lib,
   stdenv,
   fetchurl,
-  jre,
+  openjdk17,
   makeWrapper,
   replaceVars,
   coreutils,
···
   ];
 
   nativeBuildInputs = [ makeWrapper ];
-  buildInputs = [ jre ];
+  buildInputs = [ openjdk17 ];
 
   installPhase = ''
     mkdir -pv $out/{share,bin}
···
     ln -s $out/share/cytoscape.sh $out/bin/cytoscape
 
     wrapProgram $out/share/cytoscape.sh \
-      --set JAVA_HOME "${jre}" \
-      --set JAVA  "${jre}/bin/java"
+      --set JAVA_HOME "${openjdk17}" \
+      --set JAVA  "${openjdk17}/bin/java"
 
     chmod +x $out/bin/cytoscape
   '';

pkgs/top-level/all-packages.nix

···
 
   convertall = qt5.callPackage ../applications/science/misc/convertall { };
 
-  cytoscape = callPackage ../applications/science/misc/cytoscape {
-    jre = openjdk17;
-  };
-
   faissWithCuda = faiss.override {
     cudaSupport = true;
   };