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
John Chilton
4bc926d9f0
Adding script to scripts/api directory for importing workflows from
...
file paths.
2012-03-08 09:03:27 -06:00
John Chilton
de62173aff
Actually we don't want to set that environment variable, that make
...
python behave like -i every execution.
2012-03-05 15:23:28 -06:00
John Chilton
ecb256ef46
Adding db_shell.py that can be used to simplify writing command line
...
scripts against the Galaxy model/database layer or to make use of
Galaxy models in an interactive shell.
2012-03-05 12:11:53 -06:00
Dannon Baker
631cb80f59
Merged in peterjc/galaxy-central/split_blast (pull request #37 )
2012-02-28 12:26:29 -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
Peter Cock
3b3d70ce54
Not all datatype splitters write a JSON file
2012-02-16 16:22:58 +00:00
Nate Coraor
c8f4c93799
Make set_user_disk_usage.py object store-aware.
2012-02-09 13:26:14 -05:00
Nate Coraor
c43633c5cb
Pass the config file name to set_metadata.py rather than relying on a hardcoded value.
2012-02-08 11:12:10 -05:00
Nate Coraor
9aed5a36d8
Fix for dataset cleanup scripts and object store.
2012-01-31 14:07:14 -05:00
Nate Coraor
0354480bd2
Merge jdlogicman/galaxy-central-startup-integration-apis
2012-01-24 12:18:21 -05:00
Nate Coraor
61062a3ae5
Merge galaxy-central.
2012-01-18 10:34:39 -05:00
Nate Coraor
445d8494ac
Fix extra files display with object store and the distributed object store config.
2011-12-13 00:45:52 -05:00
Nate Coraor
5e96e67f1d
Hierarchical object store sample config and functional test capability.
2011-12-08 16:10:18 -05:00
Nate Coraor
d95e50dabd
Merge galaxy-central.
2011-12-07 16:06:24 -05:00
Nate Coraor
44344fe2e0
Fix the dataset controller's stderr method and add one for stdout. Link to
...
both from the dataset info page. The functional tests will now provide output
of these on tool test failure. The functional tests can now use
tool_dependency_dir as well.
2011-12-06 11:29:02 -05:00
Greg Von Kuster
17c5b27cdc
Re-engineer the datatypes registry so that it is initialized once when the Galaxy server is started, but data types can continue to be loaded throughout the Galaxy server's session (hopefully this doesn't break anything).
...
Add support for a single "import_module" to be passed to the new load_datatypes() method in the datatypes registry. This provides the ability to load a single class module from an installed tool shed repository along with a datatypes_conf.xml file included in the installed repository and pass them to the new load_datatypes() method. In the future, multiple imported modules may be allowed. The datatypes_conf.xml file included in the repository must conform to a slightly different definition than the same named file that comes with the distribution. This new definition will be documented in the Galaxy tool shed wiki.
We now have the ability to load new data types into the Galaxy server from an installed tool shed repository without restarting the Galaxy server.
2011-11-23 16:16:15 -05:00
John Duddy
753c29b445
Allow command-line creation of initial database
2011-11-18 12:41:27 -08:00
Nate Coraor
d03b63a311
Merge galaxy-central
2011-11-15 12:35:57 -05:00
Nate Coraor
24b9c8c8a7
Some fixes to actual user code to negate the need for world-writable directories and write external metadata and job stdout/stderr to the job working directory.
2011-10-31 16:15:00 -04:00
ichorny
236276b132
add actual user changes to galaxy-central
2011-10-21 14:01:48 -07:00
John Duddy
c279ecd33b
Upgrade of splitting code to do splitting in the tasks versus in the Galaxy process
2011-10-07 14:12:40 -07:00
John Duddy
a2c0328241
Merge
2011-10-07 13:25:19 -07:00
Nate Coraor
8afb807a4d
merge
2011-10-05 16:44:43 -04:00
Nate Coraor
e7180eed8f
New API scripts to do POST/PUT/DELETE without any guidance. Use like:
...
./update.py key url param1=val param2=val
2011-09-14 14:40:38 -04:00
Dannon Baker