script to submit Experiment BAM files to EBI

WS240 Models
------------

This cycle we see 3 models proposals effecting 2 classes

?Variation x 2

?Interaction x 1

More information can be found here:
http://wiki.wormbase.org/index.php/WS240_Models.wrm
added WS release number to title of submission
Warn user if it looks like -modify should be used
Fixed typo in binding_site method
Added idUnmerge to undo a merge event (not the same as a split, because the target is an existing dead entry)
More refinement of source map
Bug fix
Another one
Added D.immitus
Added D.immitus as a provisional species
extended to cope with soft-clipped alignments (which the Ensembl pipeline now reports correctly)
Pass log obj to run_script to avoid warnings
Lower-case non-reserved attribute names for GFF3
Change all sources for canonical gene set back to WormBase
this is the EBI rakefile, where compara is nowadays running
guide tree for the new compara (including named branches)
Removed addition of notes; this is now done in core GFF munging
Now only does marker positions. The other general gene decoration is now done in another script
Decorates gene lines with additional attributes (locus name etc)