Major As only customized CLARK version is only supported by UGENE, add this to the description of the corresponding tools in the Application Settings, for example:
One of the classifiers from the CLARK framework. This tool is created for workstations with limited memory (i.e., "l" for light), it provides precise classification on small metagenomes. Note that a UGENE-customized version of the tool is required.
Also, add "UGENE-customized" text to the message output by the customized tools and use these output for validation also, for example, check "UGENE-customized CLARK" for the main executable file.