Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:None
-
Story Points:3
-
Epic Link:
-
Sprint:Spring 3, Spring 4, Spring 5
Description
Situation: We are hosting our subversion repository on our own EC2. The larger size of the repository is expensive.
Task: Remove the 2bit file from the svn repository for older "legacy" genome versions, such as older versions of the human or mouse genomes. Then use the annots.xml "name" attribute to point to that same file hosted on the UCSC Genome Web (link: https://hgdownload.soe.ucsc.edu/gbdb/) and set "reference" to true (see https://wiki.bioviz.org/confluence/display/igbman/About+annots.xml for more details).
Attachments
Issue Links
- relates to
-
IGBF-2537 Enable Quickload to specify the 2bit file for a genome
-
- Closed
-
Activity
The URL's to the 2bit files were, in fact, incorrect for both of these genomes. I've fixed both URL's and tested these changes with IGB 10.1.0 and my local quickload repository. Both reference genomes/sequences load successfully, no errors in the log. Ready for testing!
SVN is down so I just tested the new URLs as custom genomes.
- E_caballus_Sep_2007 - working correctly
- A_melanoleuca_Dec_2009 - kind of working, Paige Kulzer - the url looks good, but when I try to view the genome in IGB it pauses for a while then IGB starts to load the sequence for every single chromosome, which it shouldn't do. Not sure why this is happening, but it may not be an issue if the genome is accessed through a Quickload. Could you try it on your machine and if it looks good then lets deploy the changes.
It took much longer to load the A_melanoleuca genome than it did the E_caballus genome (1.600 min vs 151.2 ms), but I'm not seeing IGB attempt to load sequences. I don't see anything out of the ordinary with the annots.xml file that might be causing this.
Reviewed with Dr. Freese - ready for deployment!
Thanks Paige Kulzer and Nowlan Freese!
I have deployed the new version of the repository and also made full and "thin" backups to this latest version, which is revision 229.
Backups are available on-line here:
See attached for a document (2bit_sizes.txt) created by Dr. Loraine which provides some more information about this task. It also contains a running list of genomes which have already been worked at the time of this comment.
My task will be to modify the annots.xml file and remove the 2bit file for each genome I've added from NCBI whose 2bit file is 100 MB or larger.