Commits

Author Commit Message Labels Comments Date
James Taylor
Fixes for biomart in the trunk.
anton nekrutenko
Trunk: Forgot the pic. Got rid of the lock. Now a picture will be updated monthly
anton nekrutenko
Trunk: Got rid of the lock. Now a picture will be updated monthly
Nate Coraor
Allow for stagein/stageout rather than relying on nfs for pbs runs.
anton nekrutenko
for Trunk: Updated gops text; added links to screencasts; made join and compare smarter so they look up column numbers from datasets
anton nekrutenko
cut for trunk
Daniel Blankenberg
Biomart: add chr to the front of X and Y when in the chrom column.
Daniel Blankenberg
Minor fix for log_event, EncodeDB should work now.
James Taylor
PBS Related Fixes.
James Taylor
Modified how the Job Manager and PBS Job Runner work. Rather than just spinning on the queue the monitor method now takes all of the items from the queue at once and moves them to a waiting list, processes the waiting list, and then sleeps. The main job manager uses an interruptible sleep so that when new jobs arrive they are dispatched immediately. This should help with processor utilization quite a bit (spinning on the queues with no sleep was pretty heavy).
Daniel Blankenberg
Add 'URL' to the list of parameters that are not sanitized. URL is used for datasources such as biomart (and hbvar soon).
James Taylor
Documentation improvements.
James Taylor
Allow passing database path and 'use_pbs' to the functional tests. TODO: This should just be able to read an INI file, far too many variables at this point.
Daniel Blankenberg
Update cron scripts to reflect the fact that ElementTree is now an egg.
James Taylor
Fix the bugs I introduced into Nate's code while splitting up job queue (PBS seems to work now in trunk).
Daniel Blankenberg
AXT to LAV does work.
Daniel Blankenberg
Updated interval2maf test data.
Daniel Blankenberg
Pushing my changes from james-wsgi branch onto the trunk. Biomart doesn't work on the trunk yet (Before or after this commit). axt to lav tool won't be functional until multiple datasets per history item is available on trunk - although I could make it so that only the lav file is generated and no fasta files, in which case it wouldn't be an issue.
James Taylor
Fix for DataToolParameter unit test.
James Taylor
Update pkg_resources.
James Taylor
Fix some doc comments.
James Taylor
Set job state properly on completion.
James Taylor
First pass at re-factoring job management: - Creating the command line has been broken up into several methods associated with 'Tool' - Creation of the command line is now done by DefaultToolAction and stored in the database (thus if the tool config changes between queueing and running of a job things will not break, and if the JobQueue was running on a different machine from the web frontend it would not need knowledge of the t…
James Taylor
Add a 'deleted' boolean column to History and Dataset. More work is still needed on the interface. It should be possible to undelete items as well. As far as purging, if a dataset is in the deleted state and not modified for a certain period of time we can purge the data file and set the state to "purged" or something similar. At this point datasets can no longer be undeleted (but we still have all the job history in the database for as long as we want).
James Taylor
Fix tool config for functional tests.
James Taylor
Cleaning up modules. Still a few stragglers that can't be easily eggified. EVERYTHING we depend on should eventually be under the galaxy module or packaged in eggs to avoid namespace problems.
James Taylor
Imports...
James Taylor
Cleaning everything up (should be working as usual)
James Taylor
More moving things around.
James Taylor
Moving some things around.
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