On 09/03/2010 16:30, Steve Taylor wrote:

To give a bit of history, we are fairly new to using Galaxy and
previously we used EMBOSS Explorer as our main web interface. With this
we found when EMBOSS releases changed lots of things broke, so we ended
up staying with EMBOSS v3. I am hoping this is not going to be true for
EMBOSS/Galaxy because they are both great tools and I want them to be
used routinely without us/users worrying if things are going to break,
especially if they are going to be incorporated routinely into workflows.
Maybe if you provide a list of problems/incompatibilities and resend
this to
the galaxy mailing list, you will get a response...

Yes please do ... I am on the Galaxy list too.

14: antigenic on data 13
An error occurred running this job: Error: Unable to read feature tags
data file 'Etags.gff3protein'

Could be you have more than one version of EMBOSS running. That looks like a pure EMBOSS error suggesting EMBOSS 6 is trying to use EMBSOS5's data directory. Should be fixable by copying the missing file.

Peter

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