On Tue, Sep 17, 2013 at 10:34 AM, Peter Cock <p.j.a.c...@googlemail.com> wrote:
> Hello all,
> Bjoern and I were talking about doing some work on more
> datatype definitions, but this raises the question about how
> to handle dependencies.
> First of all, complex datatypes in Galaxy are defined using
> Python code, so any Python dependency must be available
> to the main Galaxy process (unlike Python dependencies
> for jobs which are run on separate processes). For example,
> if I wrote GenBank/EMBL definitions using Biopython, could
> this dependency be handled via the Tool Shed?
> Second, the Python code for some datatypes may call a
> binary command line tool. For example, I was thinking of
> using the blastdbcmd binary within the BLAST database
> file format definitions to provide more useful peek
> information. Again, how could this dependency be
> handled via the Tool Shed?

Another real example: Right now I am working on wrapping
MIRA v4, and defining a custom datatype 'mira' for its own
assembly output format. I would like to handle conversion
to other formats like ACE, SAM, etc (as part of the datatype
definition) but this will mean a dependency on the miraconvert

I can instead provide a miraconvert wrapper as another
tool, but that doesn't give the full potential that using a full
datatype definition could. Is this the only sensible option
at the moment?


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