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On 07/17/2014 12:10 PM, Björn Grüning wrote:
> 
> 
> Am 17.07.2014 18:51, schrieb Peter Cock:
>> On Thu, Jul 17, 2014 at 5:45 PM, Björn Grüning
>> <bjoern.gruen...@gmail.com> wrote:
>>> Hi,
>>>
>>> I think you are right John. Datatypes have many issues in that regard
>>> as I
>>> can tell, from a few bug reports. Imho datatypes should be handled like
>>> "Tool dependency definitions". There should be only one "installable
>>> revsion".
>>>
>>> But that aside, emboss datatypes are already broken. For example asn1
>>> was
>>> added into Galaxy but it still exists in emboss_datatypes.
>>>
>>> Moreover, howto add a proper genbank datatype with sniffer, split and
>>> merge
>>> functions? Ideally, every datatype should have its own repository,
>>> but that
>>> is an overhead I would like to omit ... any other ideas?

We could use something like what I do, CI scripts and hidden .yaml files
to manage which folders get pushed to which toolshed repositories and
when. My initial version of that blindly updates things when there are
changes, but I'm working to add support for things like "create a new
versioned toolshed repository on major version # changes".

That would remove a lot of the overhead for maintaining that many
repositories.

>>>
>>> I would love to discuss that issue further, maybe a hangout with Greg
>>> and
>>> Peter?
>>>
>>> Thanks John for your input,
>>> Bjoern
>>
>> This could be high level, e.g. "other sequence file formats" repository
>> covering GenBank, EMBL, SwissProt plain text, UniProt XML, etc;
>> one for multiple sequence alignments; one for EMBOSS' own output...
> 
> That was my initial idea. Starting point is here:
> https://github.com/bgruening/galaxytools/tree/master/datatypes
> 
>> But it wouldn't be that much more work to do one ToolShed repo
>> per additional file format, would it?
> 
> Uploading and creating descriptions in the toolshed will take most of
> the time :)
> Lets see if I can use a train trip to do that ... but the problem will
> stay the same ... one repository can have multiple versions ...

And how to solve that? You're right, datatypes shouldn't have multiple
revisions since the file format should not be changing. I don't have an
answer for this either unfortunately :/

> 
>> One reason I have been meaning to do some of these is familiarity with
>> many of these formats from looking after/writing parsers in Biopython.

Peter, similar case here with BioPerl. All of my tools can output the
full range of Bio::SeqIO output formats, so having datatypes would be
great. Happy to contribute there.

>>
>> Having this done sooner rather than later ought to head off too many
>> incompatible datatype names which worries me. Is it too late to adopt
>> something like the EDAM ontology for the datatypes within Galaxy?
>>
>> Peter
>>
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- -- 
Eric Rasche
Programmer II
Center for Phage Technology
Texas A&M University
College Station, TX 77843
404-692-2048
e...@tamu.edu
rasche.e...@yandex.ru
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