On Wed, May 20, 2015 at 3:39 PM, Eric Rasche <e...@tamu.edu> wrote:
> Howdy Devs,
> I'd like to see BioPython added as an egg. I mentioned this on IRC, but it
> sort of fell off. A couple of users spoke positively about having it as a
> dependency.
> Do any of the devs have further opinions on this? Can we add it?
> Depending on BioPython would provide us with a lot of utility in the
> datatype/datatype conversion area. I'm, personally, interested in
> adding/expanding all of the datatypes from SeqIO (e.g. EMBL/
> GenBank/etc) and AlignIO (Stockholm/clustal/etc), and leveraging
> BioPython for format conversion there.
> Cheers,
> Eric

I've long thought the same thing - I think it came up in conversation
at the GCC meetings. I am however biased as one of the Biopython

From a technical point of view, while datatypes can be defined and
shared via the Tool Shed, they cannot yet use dependencies -
neither Python libraries nor command line tools (e.g. Galaxy's
dependency on samtools for BAM file handling) - which means
adding these formats to Galaxy directly and making Biopython
into a dependency of Galaxy is the easiest way to do this.


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