gmod-0.003 release candidate 2

Hello,

I am pleased to announce the availability of gmod alpha version 0.003
release candidate 2:

http://brebiou.cshl.edu/gmod/gmod-0.003-RC2.tar.bz2

If you don't remember the first release candidate, I don't blame you, it
was quite some time ago.

This release brings with it the most current chado schema and a greatly
enhanced GFF3 loading tool, gmod_bulk_load_gff3.pl, which should be able
to handle nearly all GFF3 loading needs (and it does not rely on
Class::DBI): it can now load reference/srcfeatures, it can load DNA
sequences and analysis results.

This release also contains a generic set of database triggers to allow
Apollo to read and write feature data from/to chado. While this is
still in it's infancy, it works in my hands without too much trouble.

Planned for release soon is Generic-Genome-Browser 1.63, which will have
an updated chado adaptor for use with this schema.

Since this is an alpha release, here is the (always growing) list of
items that need to be completed before I would call this a beta and bump
up to version 0.01:

- modify the bulk loader to allow 'mixed' GFF3 files (that is, containing
both analysis results and annotations). See perldoc gmod_bulk_load_gff3.pl
for more info
- modify the bulk loader to optionally spit INSERT statements in the the
files rather than the COPY FROM STDIN format as a fall back for really
big files
- modify the bulk loader to (optionally) make gene (foster) parents for
orphan transcript types.
- deprecate the use of gmod_load_gff3.pl in favor of the bulk loader
- migrate ontology loading to use go-perl (instead of Class::DBI--which
may completely eliminate the need for having Class::DBI installed
(except for turnkey))
- Flesh out Apollo stuff to be more transparent to the person doing the
installation
- Make a decision on sequence shredding and implement appropriate views
and functions

Please let me know if you have any comments or questions. I will likely
release this as 0.003 after the GMOD meeting next week.

Thanks,
Scott

Posted via an automatic script from a message
sent to the gmod-announce mailing list by
Scott Cain <cain@cshl.edu>