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 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 ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
