On Wed, May 20, 2015 at 3:39 PM, Eric Rasche <esr@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 developers.

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.

Regards, Peter