On Sun, Jul 20, 2014 at 6:23 PM, Björn Grüning <bjoern@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 Peter