[Bioperl-l] Whither Bio::FeatureIO?
Fields, Christopher J
cjfields at illinois.edu
Tue Sep 16 22:39:15 UTC 2014
It *might* be possible to set this up on Travis-CI independently on Bio::FeatureIO, which would be beneficial from a testing viewpoint (as we need to track what works w/ refactored FeatureIO vs what doesn’t).
I suppose what we need to check with a refactor (master branch) is:
1) Maintaining a sane amount of compat. with Chado. ‘Sane' meaning Bio::SF::Annotated will need to be chucked or completely reimplemented from scratch, as it is much less than sane now
2) If needed having a concurrently developed version of Chado to make it work.
It may not require much on #2 if Chado isn’t reliant on some of the less API-friendly parts of Bio::SF::Annotated (namely the heavy annotation associated with it).
On Sep 16, 2014, at 4:53 PM, George Hartzell <hartzell.george at gene.com<mailto:hartzell.george at gene.com>> wrote:
@scott, do you have test setup for the GMOD stuff?
On Tue, Sep 16, 2014 at 1:41 PM, Fields, Christopher J <cjfields at illinois.edu<mailto:cjfields at illinois.edu>> wrote:
Cool! I guess I could probably announce this as being released at some point now :)
PS - I may have a decent test environment set up for longer-term evaluation, but it would be nice to see if we can get something working with travis-ci or a smoker setup, just so I can check whether the main branch refactoring is clobbering chado (as I suspect it is).
On Sep 16, 2014, at 1:50 PM, George Hartzell <hartzell.george at gene.com<mailto:hartzell.george at gene.com>> wrote:
It took a while, but I was finally able to run my little litmus test and the good news is that it appears to pass.
I modified my ansible playbook that implements the steps described in INSTALL.Chado<https://svn.code.sf.net/p/gmod/svn/schema/trunk/chado/INSTALL.Chado> so that it uses the version of Bio::FeatureIO that is now on CPAN instead of pulling the github master.
The resulting installation ran to completion and then was able to load the yeast gff3 file:
cp /vagrant/saccharomyces_cerevisiae.gff .
gmod_gff3_preprocessor.pl<http://gmod_gff3_preprocessor.pl/> --gfffile saccharomyces_cerevisiae.gff --outfile saccharomyces_cerevisiae.sorted.gff
gmod_bulk_load_gff3.pl<http://gmod_bulk_load_gff3.pl/> --organism yeast --gfffile saccharomyces_cerevisiae.gff.sorted
and the resulting database seems to be stitched together reasonably (though I’m not a particularly informed judge of its character).
@chris thanks for the help on this!!!!
On Sat, Aug 30, 2014 at 9:24 PM, George Hartzell <hartzell at alerce.com<mailto:hartzell at alerce.com>> wrote:
Fields, Christopher J writes:
> Just a quick update on this: I released a separate Bio::FeatureIO
> release to CPAN that represents the code split out from the core
> I had to do some cleanup to get code to work and tests passing with
> some sanity. A *lot* of things were not passing tests when we
> moved this over.
> This should represent what was last working with Chado though.
> However, I haven’t officially announced anything yet b/c I would
> like to shake bugs out of it. Can either of you try this out on a
> Chado run to make sure everything is up to snuff (or at least point
> out issues)? Time depending, I would like to get something running
> on (for instance) Travis-CI, maybe including some optional
> Chado-related stuff. This would also help so that we can work on
> merging what has been done on master so that these pass the same
I can't do anything until Tuesday, but will be happy to run it through
the standard Chado build process when I get back to work.
Thanks for digging into it.
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