Dannon Baker
e660fb2591
Merged in jmchilton/galaxy-central-reports-config-enhancements (pull request #71 )
2012-11-12 12:00:18 -05:00
Dannon Baker
e4b98ca9b5
Merged in kellrott/galaxy-central (pull request #81 )
2012-11-12 11:54:45 -05:00
Greg Von Kuster
ed060ddcbe
Add the shed_tool_data_table_config to the functional test's app.
2012-11-08 11:41:21 -05:00
Greg Von Kuster
d0438ecb2f
Since tool migration scripts can be executed any number of times, make sure that no repositories are installed if not tools associated with the migration are defined in the tool_conf.xml file (or equivalent). This fix is associated only with the recently introduced Galaxy admin UI feature displaying the list of migration stages currently available. This is the way the migration process at server startup has always worked so no changes are needed in that scenario.
2012-11-07 10:51:35 -05:00
Daniel Blankenberg
e316254e28
Change indent from 3 spaces to 4 for 8171:4b62ed46e5b6.
2012-11-07 10:45:10 -05:00
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