On Jan 31, 2013, at 8:15 PM, Guest, Simon wrote:
Dear Galaxians,
We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is the expected version, as I can't find any statement about what is required in the Galaxy tool dependencies for RepeatMasker.
Anyway, when a job is submitted with no repeats, RepeatMasker 3.3.0 doesn't create the various output and summary files (.tbl, .out.gff, .out.html, .masked). This causes the Galaxy job to fail with an error message that scares the end user.
I attach a patch to handle this case, by touch'ing these files before trying to copy them. Now such jobs succeed with empty output. I think this is clearer, and certainly less scary.
Is there a better mechanism for me to contribute such fixes other than posting patches on this list?
This tool exists in the tool shed, and the best way to contribute to the patch is to contact the tool repository owner directly via email. As it happens, the tool author also frequents this list, so I've cc'd him and he may respond directly to your email.
Tool shed features are planned to make this process easier in the future.
Best, J.