[EMBOSS] Galaxy and EMBOSS

[Nigel Binns]

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
>>> _______________________________________________
>>> EMBOSS mailing list
>>> EMBOSS at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/emboss
>

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