Thanks Dave. I think I had a permission error on my bowtie2 directory. It seems to be running ok now. However the previous job is still there saying it's running but not. Is there any way to cancel these jobs or do I need to do it via the database? Thanks for the info. Shaun Quoting Dave Bouvier <dave@bx.psu.edu> on Tue, 31 Jul 2012 10:21:07 -0400:
Hello Shaun,
On 7/31/12 09:37:23.000, SHAUN WEBB wrote:
Genome indexing:
1. I realise this is just a beta feature and it will be great when fully integrated. I tried to generate bowtie2 indexes for an installed build. I can see the job appear below the table in yellow and it contains the message "...added to the job queue to be indexed with bowtie2". However it seems to just sit there, even after restarting. Should I be able to see the job under 'manage jobs'?
No, the indexing jobs are not picked up by that interface. If you click on the job ID under the 'Recent jobs:' heading, you should see a status listing of the indexing job and any sub-jobs it initiated.
2. Where are the generated indexes stored and is the .loc file automatically updated?
This can be specified with the genome_data_path option in your universe_wsgi.ini file. Currently, it defaults to tool-data/genome/<build>/<index name>/
The .loc files are updated when the job returns from a successful run, if there is no entry for that genome and index already present.
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