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Brandon King [Wed, 14 Nov 2007 03:33:04 +0000 (03:33 +0000)]
[project @ First attempt at script for configuring pipeline automatically.]
* More of prof of concept.
* FIXME: hardcoded config script path.
* Uses logging module
* Info for everything going fine.
* Error when it breaks in a bad way.
Brandon King [Tue, 13 Nov 2007 02:14:12 +0000 (02:14 +0000)]
[project @ Updated eland_config app to generate config file from fctracker app.]
* WARNING DB CHANGE: Added read_length, and advanced_run to flowcell
model in fctracker app.
* Updated eland_config app to generate config files from db instead of form.
* Currently regenerates the config file on every request. Simple flag will
cause it to re-read saved copy on disk.
* Changed URL to http://<host>/eland_config/.
Brandon King [Mon, 12 Nov 2007 22:43:35 +0000 (22:43 +0000)]
[project @ Url should be <host>/eland_config/ in this case.]
Brandon King [Mon, 12 Nov 2007 22:36:44 +0000 (22:36 +0000)]
[project @ The rest of the rename fix.]
Lorian Schaeffer [Mon, 12 Nov 2007 22:17:34 +0000 (22:17 +0000)]
[project @ Small fixes to changed directory name]
Brandon King [Mon, 12 Nov 2007 22:16:09 +0000 (22:16 +0000)]
[project @ Renamed main django project dir to ga_frontend + updated settings.]
Lorian Schaeffer [Fri, 9 Nov 2007 23:20:37 +0000 (23:20 +0000)]
[project @ Massive change to DB structure; complete library table]
Primary change to the DB is the library table and supporting changes to the flowcell table.
They should both be properly linked now; you'll have to pull species information from the
linked library field. In addition, I added a common name to the Species table. Most interface
changes are via the meta and admin classes in each model, and are fairly straightforward. I
also added databrowse support; go to /databrowse instead of /admin to play with it.
Brandon King [Sat, 10 Nov 2007 01:27:44 +0000 (01:27 +0000)]
[project @ Finished statement + additional error message]
* Now says where it wrote the config file to upon success
* Now puts more meaningful error message when user enters invalid domain/ip address.
Brandon King [Sat, 10 Nov 2007 01:20:19 +0000 (01:20 +0000)]
[project @ Updated to give more user friendly error:]
* Gives a more user friendly error when connection is refused.
* FIXME: Should include other errors as well, such as host lookup errors.
Brandon King [Sat, 10 Nov 2007 01:05:14 +0000 (01:05 +0000)]
[project @ Improved help output:]
* Automattically displays help if called with no arguments.
* Includes description and location of config files.
* Include description of command line program.
Brandon King [Fri, 9 Nov 2007 23:45:20 +0000 (23:45 +0000)]
[project @ First working version of script which retrieves eland config file from ga_frontend.]
Lorian Schaeffer [Tue, 6 Nov 2007 16:34:29 +0000 (16:34 +0000)]
[project @ Basic Library Table]
Brandon King [Thu, 18 Oct 2007 19:22:00 +0000 (19:22 +0000)]
[project @ Eland Config Saver + FlowCell Tracker DB update]
* Now saves a copy of eland config file for later retrieval.
/elandifier/config/ <-- Index of available config files
/elandifier/config/FC#####/ <-- Eland config for specific FC#
* Save record of flow cell to database.
* Form is also saved to database... which can be viewed
in /admin/
Brandon King [Mon, 15 Oct 2007 22:36:48 +0000 (22:36 +0000)]
[project @ Prototype Web-based Eland Config generator]
* Functional, but hard coded elandifier setting.py (needs updating before use).
* Using Django SVN (will be Django 0.97).
* Form currently returns to browser, will change in future.
Diane Trout [Fri, 9 Nov 2007 23:18:46 +0000 (23:18 +0000)]
[project @ add notes about what we need to do to more fully automate the pipelien]
Diane Trout [Tue, 16 Oct 2007 22:53:43 +0000 (22:53 +0000)]
[project @ handle IOErrors from xsend]
Diane Trout [Fri, 10 Aug 2007 01:19:23 +0000 (01:19 +0000)]
[project @ add script to launch copier daemon]
Diane Trout [Fri, 10 Aug 2007 00:15:18 +0000 (00:15 +0000)]
[project @ make copier a bot with logging abilities]
this now imports benderjab and uses pythons logging module to keep
track of what rsync commands have been executed.
Diane Trout [Thu, 9 Aug 2007 01:30:34 +0000 (01:30 +0000)]
[project @ start the copier script]
this contains code to deal with launching rsync against the
rsync config over on jumpgate. it checks for directories matching
stuff the sequencer tends to generate and will launch rsync processes
against directories that look like that name. (Which might be excessive)
I still need to add the bot portion
Diane Trout [Thu, 9 Aug 2007 01:29:19 +0000 (01:29 +0000)]
[project @ add __init__.py]
actually to make setup.py work you do really need the __init__.py
package flag
Diane Trout [Thu, 9 Aug 2007 01:27:02 +0000 (01:27 +0000)]
[project @ make a spoolwatcher script]
and put most of the configuration information in the script
(i really should load it from a config file at some point)
Also teach setup.py about said script
Diane Trout [Wed, 8 Aug 2007 23:56:28 +0000 (23:56 +0000)]
[project @ add a basic setup.py file]
Diane Trout [Wed, 8 Aug 2007 23:51:43 +0000 (23:51 +0000)]
[project @ Sequencer spool drive watcher]
spoolwatcher checks to see if a file named Run.completed has been
written to /gec/jumpgate/ext0 and if it has sends a message to
runner_jid. Additionally after (currently 10 seconds have passed without
data being written, after some data has been written, it'll send a
message top copy_jid)
Diane Trout [Wed, 8 Aug 2007 21:41:25 +0000 (21:41 +0000)]
[project @ tools to handle the illumina sequencer workflow]
Diane Trout [Fri, 21 Dec 2007 01:53:12 +0000 (01:53 +0000)]
This directory will host the upstream sources