On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning <bjo...@gruenings.eu> wrote:
> Hi,
> single datatype definitions only work if you haven’t defined any converters.
> Let's assume I have a datatype X and want to ship a X -> Y converter (Y -> X
> is also possible), we will end up with a dependency loop, or? The X
> repository will depend on the Y repository, but Y is depending on X, because
> we want to include a Y -> X converter.
> Any idea how to solve that?

Excellent example!

> How to handle versions of datatypes? Extra repositories for stockholm 1.0
> and 1.1? If so ... the associated python file (sniffing, splitting ...)
> should be also versioned, or? What happend if I have two stockholm.py files
> in my system?

Potentially you might need/want to define those as two different
Galaxy datatypes?

> @Peter, can we create a striped-down, python only biopython egg? All parsers
> should be included, Bio.SeqIO should be sufficient I think.

Right now, yes in principle (and this is fine from the licence point of view),
but in practise this is a fair chunk of work. However, we are looking at
this - see https://github.com/biopython/biopython/issues/349


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:

To search Galaxy mailing lists use the unified search at:

Reply via email to