Add gtf to bed converter for McCarthy lab
Parse attributes case-insensitive
add db as a parameter to the pipeline factory
change export filename to use the experiment name

The export filename will use the filename otherwise it will fallback and
use the experiments id.
Minor tweaks for Amanda
update export gff to correctly set the basename

	modified:   modules/Pipelines/lib/CoGe/Builder/GffBuilder.pm
	modified:   modules/Pipelines/lib/CoGe/Pipelines/Misc/Gff.pm
export the genome by its name in FastaBuilder
remove obsolute organism chain functions
retab OrganismView template
remove template variables from javascript
extract the javascript from the template
Fix wrong gid param to has_annotations
partially cleanup formatting
Remove debug message
reorganize file
remove use of eval
remove genome list url hack
wrap menubar login for smaller screens
Merge branch 'master' into dev