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John,

On 10/21/2013 12:31 PM, John Chilton wrote:
> On Mon, Oct 21, 2013 at 12:11 PM, Eric Rasche <rasche.e...@yandex.ru> wrote:
> Hello all,
> 
>  At my organisation's instance of galaxy, we have some connectors to
> talk to chado (inserting/removing GenBank & GFF files, etc).
> 
>> That sounds awesome! Is that open source or are there plans to make
>> this available?
> 

Yes! Parts of it are already open source, and parts of it are scheduled
to be.

The perl scripts I use in galaxy mostly wrap a Chado library I threw
together. You can see it/fork it here.

https://github.com/erasche/charm

It's in the process of being re-written, but handles most of the stuff
you'd want to do with Chado like creating new instances for new users,
backing them up, and cloning them. The gmod*.pl are just what are
distributed with Chado. Nothing special there. Eventually I'll rework
those and distribute them with galaxy config files.

> 
> However, for one of the workflows we plan to use, there is a script
> which must be run which has no input files and no output files
> (gmod_add_organism.pl, for those curious). This script *must* be run
> before another script is run (gmod_bulk_load_gff3.pl), or the database
> insert will fail
> 
> So my question is:
> Is there an easy way to specify dependencies when they depend on
> external factors, rather than just input/output files?
> 
>> As far as I am aware there is no such mechanism in place. I would
>> create a Trello issue if you feel this should be added - it is
>> certainly not an unreasonable request. My sense however is the Galaxy
>> concept of a tool and workflow are very coupled to file inputs and
>> outputs at this time, so I am not certain we will be able to get to
>> this request quickly.
> 
>> For now, my recommendation would be just to use a dummy input and
>> output file. You can even create a file type that is only used for
>> this purpose to limit confusion. Can you find some logging statements
>> or something to populate this file with?
> 
>> Hope this helps and let us know if there are any additional questions,
>> -John

Okay. If there's no mechanism in place that's fine. I can surely find
some logging output (to put into a file and use that to couple dependencies.

I've created a trello card, as per your request, but this is really a
low priority issue.
https://trello.com/c/h5qZlgU8/1201-allowing-workflow-step-dependencies-when-no-input-output-files-exist

Thanks,
Eric

> 
> 
> If there isn't a generalised mechanism to do this, should I just list
> input and output files that are never actually created or removed?
> 
> Cheers,
> Eric
> 
>> ___________________________________________________________
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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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