Daniel Blankenberg
bbeed4dc0b
Use check_python() to verify python version in set_metadata.py instead of hardcoded minimum version check.
2012-11-07 10:35:56 -05:00
Kyle Ellrott
4e8d938ff7
Adding the initial componenents of an extended metadata system for datasets.
...
The idea behind an 'extended metadata' for datasets is to provide a mechanism to encode
and index user generated metadata and keep it attached to files. Users can provide a
JSON style data structure which will then be indexed and stored. Later this index can
be used to search and discover datasets via a pseudo-formal schema.
This patch introduces the tables, and makes it possible to inject user metadata into a file
load using the 'extended_metadata' field in the query.
2012-10-28 00:28:42 -07:00
Dave Bouvier
cc608c31b2
Updated migration script to reference repository with correct use of tool dependency tag sets.
2012-10-25 13:25:39 -04:00
Dave Bouvier
c968460662
Migrate Picard tools to the tool shed.
2012-10-24 11:09:20 -04:00
Scott McManus
a0afee842e
Re-commit new /api/folders section
2012-10-15 18:09:25 -04:00
Scott McManus
0148eabc72
Backout
2012-10-15 17:53:37 -04:00
Scott McManus
954e96fc34
Added /api/folders. The api_folders configuration variable controls access to it (and is False by default).
2012-10-15 17:29:29 -04:00
Daniel Blankenberg
94a2f94529
Fix minor typos in db_shell.py
2012-10-11 16:43:37 -04:00
Nate Coraor
9213c344db
Fix reporting in the set_user_disk_usage.py script.
2012-10-03 13:40:54 -04:00
Nate Coraor
9ab95a9fa9
Fix passing of job name when running jobs as a system user.
2012-10-03 11:51:07 -04:00
Nate Coraor
1e2256fe0e
pgcleanup: Print a useful message if no options are given.
2012-10-01 13:45:37 -04:00
Nate Coraor
8193489dda
pgcleanup/set_user_disk_usage: set usage to 0, not null, when the user has no active data.
2012-09-28 16:11:38 -04:00
Dave Bouvier
c2eeee7b9f
Migrate BWA to the tool shed.
2012-09-28 15:35:44 -04:00
Nate Coraor
caa06bbc20
Allow Postgres users to update user disk usage with a fast wCTE rather than a slower computation in Python.
2012-09-28 14:30:10 -04:00
John Chilton
c3e99bc384
Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.
...
Added flag (--sync-config) to run_reports.sh script that will cause it to synchronize the database connection and file path properties in reports_wsgi.ini with those in universe_wsgi.ini prior to starting paster app.
Allow specification of reports configuration directory mirroring similar extensions previously accepted for universe config and run.sh
Added usage documentation to run_reports.sh.
Added extension points to tweak pid and log location for reports application via environment variables.
2012-09-21 22:04:15 -05:00
Dannon Baker
ba6114ca3e
Fix create_all_fasta_loc to work when inspect_dir is not set.
2012-09-18 20:49:29 -04:00
Nate Coraor
459d3a2c1d
More pgcleanup.py fixes and addition of cleanup event tables for library items.
2012-09-17 12:51:17 -04:00
Nate Coraor
71d7f7c132
Distributed object store fixes for pgcleanup.py.
2012-09-11 12:22:03 -04:00
Nate Coraor
0e1b041cde
Bug fixes for pgcleanup.py
2012-09-10 16:59:33 -04:00
Nate Coraor
c8e49cdd6d
Bugfix for pgcleanup.py
2012-09-10 14:07:05 -04:00
Nate Coraor
e19092e9c5
Add a dataset cleanup script that's optimized for (and compatible only with) PostgreSQL 9.1+. Also add a bunch of tables for logging all cleanup events, which makes reversing such events trivial.
2012-09-10 12:03:23 -04:00
Richard Park
6839829211
Cleaned up codebase for attempting adding api additions to the galaxy main branch
2012-08-03 02:09:05 -04:00
Richard Park
e6d5c55c89
Updated notes on how to run api/workflow_execute_parameters.py
2012-04-10 23:00:41 -04:00
Richard Park
412f779f76
Updated scripts for API workflow enhancements and changing workflow parameters programatically
2012-02-01 16:21:38 -05:00
Dannon Baker
3d5fd7b5e2
Migrate NCBI Blast+ (and blastxml) to the toolshed.
2012-08-17 11:35:31 -04:00
Nate Coraor
5752c297d9
Merged in jmchilton/galaxy-central-configuration-directory (pull request #44 )
2012-08-15 10:57:14 -04:00
Nate Coraor
a7f4a7534a
Merged in jmchilton/galaxy-central-preseeding (pull request #38 )
2012-08-15 10:54:50 -04:00
Carl Eberhard
d97ada4bb5
minor docstring adds in /scripts
2012-08-03 13:31:48 -04:00
Greg Von Kuster
7992dfa449
Another change to installed changed revision for the freebayes tool migration process.
2012-07-13 12:53:42 -04:00
Greg Von Kuster
2c87a63983
Change ethe installed changed revision for the freebayes tool migration process.
2012-07-13 12:50:29 -04:00
Greg Von Kuster
5c8fe01456
Migrate the freebayes tool out of the Galaxy code distribution.
2012-07-10 16:23:34 -04:00
Enis Afgan
fa1959b579
Fix API history purge; a few documentation corrections
2012-06-18 14:53:02 +10:00
John Chilton
55b451dcf4
Fix a typo.
2012-05-24 07:47:14 -05:00
John Chilton
7ba16d90ad
Augment run.sh to search for the optional environment variable
...
GALAXY_UNIVERSE_CONFIG_DIR. If this is set, before Galaxy is launched
the directory specified by the environment variable is searched for
ini config files. These files are merged into a single configuration
structure and written back out as universe.ini.
This should allow for a more modular configuration of Galaxy. The
files are merged in lexiographic order and later files can override
properties specified ealier on. If a consistent naming scheme is used
this can be really useful:
As an example, one might specify the files as such:
000_galaxy_defaults.ini
000_default_sqlite_config.ini
100_institution_specific.ini
500_job_runner.ini
500_webapp_0.ini
500_webapp_1.ini
500_instance_specific.ini
500_available_postgres.ini
2012-05-04 00:12:43 -05:00
Greg Von Kuster
2632e05024
Add a running_functional_tests config setting.
2012-04-18 16:20:17 -04:00
Dannon Baker
ecf83a5be5
Merged in peterjc/galaxy-central/split_blast2 (pull request #41 )
2012-04-18 07:56:05 -04:00
Peter Cock
e6628b9b66
Update scripts/check_python.py (Python 2.4 not supported)
2012-04-17 13:48:51 +01:00
Nate Coraor
23919dfbc6
Fix job manager/handler shutdown, functional tests due to referer -> redirect rename, and check_galaxy script for dataset display -> html table change.
2012-04-16 14:56:24 -04:00
Nate Coraor
35dd4e1ef9
Fix for cleanup_datasets.py when database_connection is the uncommented default in the config file.
2012-04-16 10:07:10 -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
Nate Coraor
3493f9ebcd
Fix the data transfer script to work with new API library content ids.
2012-03-30 09:51:04 -04:00
Greg Von Kuster
46c597b5c3
Change new functional test flags to conform more closely to previous command line flags
2012-03-30 09:36:21 -04:00
Greg Von Kuster
816a43c2f9
Enhance the functional test framework to support testing tools contained in installed repositories that were not migrated from the Galaxy distribution. To test these tools, use: sh run_functional_tests.sh --installed
2012-03-29 15:02:36 -04:00
Greg Von Kuster
60c0bdf17b
Enhance the functional test framework to support tools migrated from the distribution and installed from the tool shed. To test these tools, use: sh run_functional_tests.sh --migrated
2012-03-29 12:03:14 -04:00
Greg Von Kuster
3c5f027a73
Enable the installation of the emboss_5 repository from the tool shed under the condition that any of its contained tools are defined in a local tool_conf.xml file.
2012-03-21 16:53:26 -04:00
Dannon Baker
369f144223
Merged in jmchilton/galaxy-central-preseeding/workflow_import_menu_api (pull request #40 )
2012-03-21 09:48:47 -04:00
John Chilton
1c37cb28ca
Augment workflow import api to allow add_to_menu argument which (when
...
true) adds imported workflow to user's workflow menu. Augment api
example script to take in an optional fourth parameter --add_to_menu
to enable this.
2012-03-19 12:13:59 -05:00
Greg Von Kuster
7ebdf0f24a
More fixes for handling mor ethan one non-shed tool anel config when installing tools migrated from the distrobution to the tool shed.
2012-03-15 14:12:59 -04:00
Greg Von Kuster
628b6ea82d
Use an odict instead of a dict when acquuiring elements for generating entries for the migrated_tools_conf.xml from the InstallManager, and handle multiple proprietary non-shed tool panel configs with the InstallManger.
2012-03-15 11:47:46 -04:00
Greg Von Kuster
19862fd03b
Update the integrated_toon_conf.xml file only if a new config setting is True. This keeps things that start up the app (like functional tests) from updating the file.
2012-03-14 17:21:03 -04:00
Daniel Blankenberg