I'm running EMBOSS 6.2.0 (and Jemboss via JWS) with the latest patch
applied and EMBOSS Explorer (v2.2.0) without any problems. The only
issue I've experienced is that the link to the EMBOSS help files is
broken The workaround is to copy the EMBOSS HTML help files to the
location EE expects to find them - which is not where the current
release of EMBOSS is places them :-)
Nigel
On 09/03/2010 16:30, Steve Taylor wrote:
Hi Hans,
I notice in the Galaxy distribution there is support for EMBOSS 5.
Does anyone
on this list know if there planned support for EMBOSS 6? We have
found using
our local installation of EMBOSS 6 that a few tools don't work.
which tools don't work?
We are using most of the EMBOSS 6.1.0 tools in or local galaxy
server. And I
don't remember running into problems with the galaxy emboss 5 tool
definitions (ie emboss_*.xml files).
Ok. That's good to know.
I haven't checked EMBOSS 6.2.0, but I guess there are just a few
additions
(based on the release notes) you need to make. Generally speaking:
EMBOSS
tools are pretty stable.
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...
Maybe I was a bit unlucky because I tried a few more tools and
generally things are ok. A couple of minor issues I came across:
* antigenic
(ran but gave an error)
14: antigenic on data 13
An error occurred running this job: Error: Unable to read feature tags
data file 'Etags.gff3protein'
* etandem produced two outputs (not exactly an error but I wondered if
it was a misconfiguration in the xml)
there may be more ...
Your email answers my question that in general EMBOSS 6 is compatible
with EMBOSS 5 but probably some minor tweaks may be required for
certain tools. It would great if some form of unit testing could be
employed to check compatibility with new builds.
Thanks,
Steve
Hans
Is there a person who maintains the Galaxy/EMBOSS configuration?
I know this is *really* a Galaxy question but I posted this to the
Galaxy list
but haven't had any response so far. :-)
Thanks,
Steve
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