Awaiting resolution regarding ssh port 22 error; will complete BED12 to BED14 conversion when error resolved and able to access HPC cluster.

Port 22 Host error resolved via UNCC IT.

Attempting to resolve console error on startup:

14:54:52.113 ERROR o.l.i.quickload.util.QuickloadUtils - Could not read annots.xml or this file was empty. Skipping this genome version for quickload site file:/Users/jilljenkins/Dropbox/Data%20Management%20for%20Quickload/genomes/quickload/C_elegans_Feb_2013/

Resolved console error: corrected annots,xml file

Successfully added to DropBox - tested in IGB. Systems check: 1 exception, IGB not populating most recent genome on initialization (Feb 2013). Will continue working on it.

I have reviewed this addition in IGB - all 'seems' well except the newest assembly is not generating first once the species has been selected.

Make sure that this newest assembly is selected when the user clicks the C. elegans image in the IGB start (home) screen. Check the IGB console for clues - there may be some error messages.

Seems operational now - unsure of malfunction experienced yesterday.

Modify annots.xml to ensure that browser opens to the genome directory (not UCSC site) when user clicks "i" next to RefSeq Genes data set listing in Data Access Panel.

Also, modify previous C. elegans release annots.xml to ensure the same thing.

Can use latest H. sapiens genome version annots.xml as a guide for how to do this. Also review documentation.

The link to the genome directory does not exist until someone with privileges actually adds the new genome to the QL. Is there a work-around?

Modify "url" attribute for the gene annotations file to ensure that when a user clicks "i" in the IGB interface it will open the genome directory in the user's browser. See annots.xml files for other genomes for syntax examples.

Answer your question. Take a look. If it still doesn't make sense, leave it for Thursday & I'll explain then.

I corrected the issue by reading the documentation and adding the directory name to the url attribute, mirroring other genomes.

Committed to svn:

reg-10-23-251-93:quickload aloraine$ svn ci C_elegans_Feb_2013 -m "Add C. elegans Feb 2013 (WBcel235/ce11) genome assembly and gene models"
Adding C_elegans_Feb_2013
Adding (bin) C_elegans_Feb_2013/C_elegans_Feb_2013.2bit
Adding (bin) C_elegans_Feb_2013/C_elegans_Feb_2013_refGene.bed.gz
Adding (bin) C_elegans_Feb_2013/C_elegans_Feb_2013_refGene.bed.gz.tbi
Adding C_elegans_Feb_2013/HEADER.md
Adding C_elegans_Feb_2013/annots.xml
Adding C_elegans_Feb_2013/genome.txt
Transmitting file data ......done
Committing transaction...
Committed revision 89.

Issue is now complete.
Re-assigning to original developer for record-keeping.