Remove GOBYWEB_SERVER_SIDE_2.1.1 from master branch.
Fix wrong import in Biomart.groovy in ENSEMBL_ANNOTATIONS_2.0.
Fix wrong import in Biomart.groovy in ENSEMBL_ANNOTATIONS_2.0.
Fix gzip compression when creating the archive of files downloaded with Biomart (ENSEMBL_ANNOTATIONS).
Exclude snp dataaset for non-human organisms. Fix download and merge of chromosome files when filtering by chromosome is enabled.
Fix inverted check in Biomart.groovy.
Fix fetchFileWithRetries in Biomart.groovy (ENSEMBL_ANNOTATION_2.0).
Upgrade version of ENSEMBL_ANNOTATION_2.0 to 2.1.2.1 to force re-installation on the artifacts repository.
Fix parameters reading in align-bisulfite-both-strands.sh.
Fix PARALLEL_LAST invocation from LAST_BISULFITE_V2_ARTIFACT. Add safety assignment in PARALLEL_LAST script to manage the case when PAIRED_END_ALIGNMENT is not passed as parameter.
Remove PAIRED_END_ALIGNMENT from run-parallel mode parameters in PARALLEL_LAST script.
Add GOBYWEB_SERVER_SIDE_2.1.1 resource to push results of process sample on the cluster.
Fix local file copy operation in ProcessSamples.groovy.
Fix fetchFileWithRetries in Biomart.groovy (ENSEMBL_ANNOTATION_2.0).

Conflicts:
	plugins/resources/ENSEMBL_ANNOTATIONS_2.0/Biomart.groovy
Add memory settings to jvm execution in the artifact scripts.
Remove shift command from plastal.sh.
Rename run-goby to run_goby (see http://www.gnu.org/software/bash/manual/bash.html#Shell-Functions).
Rename run-R to run_R (see http://www.gnu.org/software/bash/manual/bash.html#Shell-Functions).
Increase Goby_2.3.3 version to force re-installation on the artifact repositories.
Increase R_2.15.3 version to force re-installation on the artifact repositories.