Fix annotation source variable scope
Advance version number
Fix configuration for annotation options: option type is required
Correct paths of environment variables
Add indexed genome artifact dependency and fix reference in analysis script to the indexed genome
Add annotation classes for 3' and 5' UTR to Ensembl Annoations.
Fixed syntax issue with methylation regions auto-install
set flag to create all types of annotation files
Fix zip name in LAST_287.
Add filename when downloading the zip file in LAST_287.
revert ENSEMBL_ANNOTATIONS_1.0 to original working version
create ENSEMBL_ANNOTATIONS_2.0 to start adding new annotation classes such as UTRs, introns etc etc
Install ENSEMBL_GENOMES v. 1.0 using fetch URL scripts.
Merge remote-tracking branch 'origin/master'
Fix PLUGIN_GROUP_ALIGNMENTS constant in CONTAMINANT_EXTRACT.
Fix run_minia function in MINIA_2013_1.4961.
Fix  minia output filename in MINIA_2013_1.4961.
Add Lucene Indexes to CONTAMINANT_EXTRACT's output schema.
Add Jar file for goby 2.3.1 (with timestamp version).
Switch global_goby.jar to GOBY_2.3.1
Add Goby 2.3.2 pre-release
Merge branch 'master' of bitbucket.org:campagnelaboratory/gobyweb2-plugins