Creating a blue line project with a sequence that is not in FASTA format results in 505. 
Now it will bypass the error and inform the user about it.



git-svn-id: http://svn.dnalc.org/ga/pipeline@772 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- better message informing the user, about sequence not being in the tight format


git-svn-id: http://svn.dnalc.org/ga/pipeline@773 8e20c4c2-b435-4367-b5b9-847ebbf7797d
-edited the tooltips content
- added 'city' field to step6.html (reviewing your submission) and view.html (was missing)


git-svn-id: http://svn.dnalc.org/ga/pipeline@774 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- fixes on blue line project names (removed projects are actually marked as archived)



git-svn-id: http://svn.dnalc.org/ga/pipeline@775 8e20c4c2-b435-4367-b5b9-847ebbf7797d
minor grammar fixes to tooltips


git-svn-id: http://svn.dnalc.org/ga/pipeline@776 8e20c4c2-b435-4367-b5b9-847ebbf7797d
fixed variable which was causing this page to break


git-svn-id: http://svn.dnalc.org/ga/pipeline@777 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- enabled CUFFDIFF 


git-svn-id: http://svn.dnalc.org/ga/pipeline@778 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- ignore some benign errors in the error log


git-svn-id: http://svn.dnalc.org/ga/pipeline@779 8e20c4c2-b435-4367-b5b9-847ebbf7797d
Updates to the export to GB function:
- GBManager: different way to getting the primer info to support cocktail primers, host (as common name) and isolation source now also sent to the annotation module to annotate the sequence in line with request from NCBI
- Annotation.pm: now gets the host and isolation source from GBManager and inserts these values into the annotion
- PRIMERS: new structure to support cocktail primers
- BARCODING_PROJECT: commented the BLI project type (no BioProject ID yet)
- .comp/counties: modified "United States" to "USA" in line with requirements from NCBI
- index.html: removed the instruction for primers as this is very trivial now
- view.html: included view for the common name, removed 'reverse primer', changed 'forward primer' to 'primer' (they only select the primer one time now)
- step6.html: same changes as view.html
- step4.html: added support for cocktail primers. added field for 'common name', updated field for 'isolation type' - these are needed for correct annotation


git-svn-id: http://svn.dnalc.org/ga/pipeline@780 8e20c4c2-b435-4367-b5b9-847ebbf7797d
updated contact information


git-svn-id: http://svn.dnalc.org/ga/pipeline@781 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- set the project as Urban Barcode Project by default (for now)
- added comments


git-svn-id: http://svn.dnalc.org/ga/pipeline@782 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- view cufflinks outpur
- get status of the jobs from the control panel



git-svn-id: http://svn.dnalc.org/ga/pipeline@783 8e20c4c2-b435-4367-b5b9-847ebbf7797d
minor fix: remove the 'lc' function on the state name when creating the source modifier table


git-svn-id: http://svn.dnalc.org/ga/pipeline@784 8e20c4c2-b435-4367-b5b9-847ebbf7797d
All changes related to animal toggles for the redline
scontent.css: style definitions for the matrix table which shows the species used to train the individual gene predictors
console.html: renamed the tool 'Snap' to 'SNAP', introduced custom names for the external browser link based on the sample type (ex: FlyBase Browser)
create_project.html: organism classes are now described/labeled in singular form, added tooltip matrix to describe the species used to train each gene predictor
create_project.js: toggle the tooltip for plants and animals
console.js: edited titles for the tools SNAP and RepeatMakser



git-svn-id: http://svn.dnalc.org/ga/pipeline@785 8e20c4c2-b435-4367-b5b9-847ebbf7797d
fixed formatting for species names in matrix


git-svn-id: http://svn.dnalc.org/ga/pipeline@786 8e20c4c2-b435-4367-b5b9-847ebbf7797d
Changed the 'host' field in the annotation from common name to scientific name (removed all functionality to collect and show common name, we don't need it).


git-svn-id: http://svn.dnalc.org/ga/pipeline@787 8e20c4c2-b435-4367-b5b9-847ebbf7797d
Added greenline to homepage


git-svn-id: http://svn.dnalc.org/ga/pipeline@788 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- added changes to cuffdiff, which supports replicates (two for now)
- retrieve the size and lastmodified attributes for the iRODS files
  = for this I added 2 new columns to table ngs_data_file:
	last_modified timestamp without time zone
	file_size integer DEFAULT 0





git-svn-id: http://svn.dnalc.org/ga/pipeline@789 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- added a function to show nice bytes (KB, MB, GB)
- updated the trimmer tool


git-svn-id: http://svn.dnalc.org/ga/pipeline@790 8e20c4c2-b435-4367-b5b9-847ebbf7797d
- trimming work in the manage_data window


git-svn-id: http://svn.dnalc.org/ga/pipeline@791 8e20c4c2-b435-4367-b5b9-847ebbf7797d