[EMBOSS] Galaxy and EMBOSS

[Steve Taylor]

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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>