Hi Matt,
remote launch of HMMER3 search is not yet supported.
I've created a corresponding issue in the bug tracker:
https://ugene.unipro.ru/tracker/browse/UGENE-418After this issue is resolved, it will be possible to run HMMER3 remotely from Workflow Designer.
Meanwhile you can try using a bit out-dated HMMER2. I've attached the workflow schema.
Please note that currently the default public UGENE remote service has rather limited hardware capabilities. There is another free public cluster available till September. Add this address to the list of your remote machines:
https://ugene.unipro.ru/fcp/remote/rservice/engineUser registration is here:
https://ugene.unipro.ru/fcp/remote/user