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
binary.
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?
Regards,
Peter
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