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.

   --Dave B.
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