On Mon, Oct 21, 2013 at 12:11 PM, Eric Rasche <rasche.e...@yandex.ru> wrote:
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> 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
> 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,
> 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?
> - --
> Eric Rasche
> Programmer II
> Center for Phage Technology
> Texas A&M University
> College Station, TX 77843
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