Nate Coraor
a2e93ebccd
Reorganize object store options in sample config file.
2013-08-28 16:08:21 -04:00
Carl Eberhard
eb5a3bcb4d
Visualization framework: update universe_wsgi vis plugin entry with absolute path explanation
2013-08-06 17:15:17 -04:00
Carl Eberhard
17addb206f
Visualizations framework: PluginFramework class, serving static and template files from plugins
2013-08-06 15:02:10 -04:00
Nate Coraor
3036d2e2f5
Merge stable.
2013-08-02 16:39:52 -04:00
Jeremy Goecks
8944c1ac30
Move welcome_url setting to 'UI Localization' section of the config file.
2013-07-29 22:38:17 -04:00
Jeremy Goecks
a1714c4ad2
Add and document welcome_url config option.
2013-07-29 17:36:39 -04:00
Carl Eberhard
6ad1eb0b98
Visualizations registry: turned off by default in main .ini
2013-07-18 16:27:38 -04:00
Carl Eberhard
e98313a66f
Visualizations registry: break visualizations_conf.xml into one xml file per visualization and place in config/visualizations
2013-07-18 15:52:38 -04:00
Dannon Baker
7bf8e86c73
Make default ami configurable via universe
2013-06-30 01:26:31 -04:00
Dave Bouvier
376e106f42
Add the threadpool_kill_thread_limit option to universe_wsgi.ini.sample.
2013-06-24 15:43:14 -04:00
Carl Eberhard
df1927422c
Visualizations framework: allow users to associate custom visualizations with models, datatypes, etc. via an xml configuration file (visualizations_conf.xml)
2013-05-17 14:45:07 -04:00
Dave Bouvier
c77ec36e9b
Enable dynamic configuration of message box content and visibility in the wsgi .ini file. Display the configured brand, if any, in the <title> element.
2013-05-07 11:22:38 -04:00
Dannon Baker
68065e1238
Remove set_metadata_externally from the universe sample.
2013-05-06 13:07:31 -04:00
Daniel Blankenberg
98a51470f2
Allow old-style display applications to be disabled.
2013-03-22 11:43:42 -04:00
Daniel Blankenberg
1c9861eca2
First pass at a plugable Data Manager. Data Managers can be defined locally or installed from a Tool Shed. TODO: Display Data Manager information in the Tool Shed. Do not install Data Managers into Tool Panel. Add tests. Write Docs.
2013-02-14 15:13:06 -05:00
Nate Coraor
9b7775be03
Define and implement job destinations, an improved method for defining resources on which Galaxy will run jobs. Functionality is similar to the current system configured via "URLs" in the Galaxy config file, but job concurrency limits on a per-destination basis works (whereas per-URL limits were broken). Sample configs for the new destination system can be found in job_conf.xml.sample_*. Also, renamed ClusterJobRunner to AsynchronousJobRunner, moved worker threads to BaseJobRunner and significantly expanded both of these classes. Updated the tasks, local, lwr, and pbs runners to use destinations, and to inherit from AsynchronousJobRunner, drmaa coming shortly. This should be entirely backwards-compatible, so if you update to this revision and change nothing, your jobs should all still run exactly as they have before. Regardless, it is not recommended that you upgrade your Galaxy instance with jobs running unless you are willing to risk losing those jobs.
2013-02-07 15:31:09 -05:00
Jeremy Goecks
5a7dbec27d
Make Galaxy Q&A URL optional and disable by default.
2013-01-03 09:43:53 -05:00
Nate Coraor
ab7010d999
Add more featureful job limiting and optimize the query for checking whether
...
jobs are ready to run. Input dependency checks are now performed via SQL
rather than walking up the object chain. Limits on the number of jobs a user
can run can now be set across the entire instance and a job runner URL.
Quota checks at job runtime are only performed once, after limit checks. If a
user is over quota, jobs are moved to a "paused" state. Once the user is under
quota, jobs can be unpaused and continue to run (once this UI is added in
another commit, shortly). This obviates the need for quota checks on every
job, on every queue cycle.
When a job's input dataset errors, the job (and all jobs dependent upon that
job) are no longer errored. It will then be possible to remap a job to new
inputs to allow execution to continue from the point of failure. Commit for
that is also coming shortly.
2012-11-13 15:00:55 -05:00
Greg Von Kuster
a2e5b2fe77
Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTableEntries that should have been persisted to the XML file were not being handled correctly.
2012-11-07 16:36:28 -05:00
Nate Coraor
fa755ee63c
Allow for overriding app.config.track_jobs_in_database.
2012-09-11 14:58:13 -04:00
Remi Marenco
9a24592eaa
Added links to BioStar in the Help Menu and in tool forms + When asking to create a new post from galaxy tool form, tag is automatically fulfilled with the name of the tool + Added the url as global variable in universe
2012-09-09 17:13:00 -04:00
Jeremy Goecks
a296c1e0dc
Do not use enable_tracks or enable_pages options anymore; visualizations and pages are enabled for all instances.
2012-08-24 18:43:33 -04:00
Daniel Blankenberg
bb15315fed
Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites.
2012-08-22 12:35:23 -04:00
Enis Afgan
47b63cbf91
Add the ability for Galaxy's ObjectStore to use OpenStack's SWIFT object store as the backend data storage
2012-08-14 10:04:25 +10:00
Nate Coraor
81a8350996
Document user_job_limit
2012-07-27 10:57:29 -04:00
Nate Coraor
2fc9c6312e
Add links to terms and conditions.
2012-07-12 14:05:55 -04:00
Jeremy Goecks
577041c6b6
Put myExperiment URL in config's Beta features location.
2012-06-11 15:22:51 -04:00
Nate Coraor
28d7cb586a
Fix an artifact left over from an incomplete merge
2012-05-23 12:12:13 -04:00
Dave Bouvier
5ece871d40
Added option to download pre-built indexes from galaxy servers.
2012-05-18 09:50:35 -04:00
Jeremy Goecks
9c4d8cf2ea
Merged in fbacall/galaxy-central-myexp-integration (pull request #45 )
2012-05-10 16:27:33 -04:00
Dave Bouvier
ee9bacb494
Add admin tool to download and index a reference genome.
2012-05-10 12:55:29 -04:00
Jeremy Goecks
049891cc92
Remove enable_api flag; API is now enabled by default and cannot be disabled.
2012-04-11 14:45:44 -04:00
Dannon Baker
68c9d80fe8
New config option, and change in default behavior regarding dataset path display in View Details. Administrators can now *always* see the full path, and if the expose_dataset_path option is True, so can regular users.
2012-04-10 16:46:49 -04:00
Nate Coraor
1c676804f1
Allow multiple output file collection from the job_working_directory.
2012-04-03 22:07:19 -04:00
Nate Coraor
279ef87834
Allow job handlers to be exempted from the default random choice pool.
2012-03-31 10:06:43 -04:00
Nate Coraor
0e65233431
Allow for job handler selection based on job params (like source).
2012-03-30 14:10:45 -04:00
Nate Coraor
fd3505ceeb
Support multiple job runners by creating a job manager that designates a job handler to run jobs, thereby avoiding the "new job" race condition.
2012-03-29 17:25:56 -04:00
Finn Bacall
0c2d59d1a3
Made myExperiment URL configurable
2012-03-26 13:40:42 +01:00
Daniel Blankenberg
eed27b829a
Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed.
2012-03-23 13:41:01 -04:00
Nate Coraor
be0f3bb1d8
Change the hardcoding of UCSC servers to a config file option, and remove the dependence on ucsc_display_sites, so any display server can be allowed. If you've modified your remoteuser.py, beware the merge.
2012-03-16 11:16:49 -04:00
Dannon Baker
7ec78e35af
Add config option (sanitize_all_html, still enabled by default) to control strict dataset html output sanitization.
2012-03-05 12:00:53 -05:00
Dannon Baker
351ff6bec3
Cloud launch basics.
...
TODO: Tons of help text, shift instance dns wait to page level. pkey direct download.
2012-02-29 11:58:22 -05:00
Jeremy Goecks
85f1850585
Enable Pages and Trackster by default in universe.
2012-02-29 09:53:56 -05:00
Jeremy Goecks
784ded84ae
Parameterize per-tool job runners so that parameter name/value pairs can be used to define multiple runners per tool. Documentation is in sample universe file. Add 'params' column to jobs table to store job parameters, and add source parameter for all jobs initiated in Trackster.
2012-02-28 17:50:26 -05:00
Greg Von Kuster
e0942033ba
The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed.
2012-02-28 11:38:08 -05:00
Dannon Baker
2e6e3b2118
Preliminary autopacking for javascript.
...
Disabled by default (pack_scripts in universe_wsgi.ini) and the packed scripts are still in the distribution, to be removed at some point.
2012-02-24 17:47:47 -05:00
Dave Clements
150cb55997
Changed the default new user mailing list from galaxy-user to galaxy-announce, which is a much lower volume. Also added text to link to wiki page with all mailing lists.
2012-02-01 21:25:41 -08:00
Nate Coraor
302b1600a5
Add tool_dependency_dir to the sample config.
2012-01-23 12:29:00 -05:00
Nate Coraor
c362e6202e
A bit more actual user cleaning.
2012-01-18 14:34:00 -05:00
Nate Coraor
61062a3ae5
Merge galaxy-central.
2012-01-18 10:34:39 -05:00
Nate Coraor