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?


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Attachment: galaxy-repeatmasker-agr.patch
Description: galaxy-repeatmasker-agr.patch

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