galaxy-central /

Filename Size Date modified Message
config/plugins/visualizations
contrib
cron
database
display_applications
doc
external_service_types
lib
locale
openid
scripts
static
templates
test
test-data
tool-data
tools
43 B
Create unit test directory with example test. Enable coverage report generation of unit tests (run_unit_tests.sh will automatically add --with-coverage to nosetests call if coverage is on the path, coverage report can than be generated with 'coverage html' and viewed at htmlcov/index.html). Update .hgignore to reflect these changes.
1.9 KB
Visualizations framework: PluginFramework class, serving static and template files from plugins
361 B
Added tag release_2013.08.12 for changeset 1ae95b3aa98d
11.1 KB
Reindented license text to make it render better at bitbucket.
815 B
Update README.txt to reflect Python 2.5 is no longer supported.
3.5 KB
Typo in documentation
4.9 KB
GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time."
60 B
Allow command-line creation of initial database
55 B
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.
20.8 KB
Results display updated for barcoded uploads
22.8 KB
Pull from galaxy-dist
1.9 KB
Add the config for the demo sequencer.
7.1 KB
Provide mercurial as an egg for tool shed operations.
521 B
Object Store: Store the backend object store's ID in the database when using the distributed object store.
1.8 KB
Pull from galaxy-dist
234 B
Renamed sequencer to external_service and sequencer_type to external_service_type.
146 B
Upgrade of splitting code to do splitting in the tasks versus in the Galaxy process
2.2 KB
Improve structure of invalid tools dict. Clarify summary and detailed log output. Add check for required environment variables.
4.6 KB
Condor runner: Allow for per-destination ClassAd query params, don't delete the submit file if submission fails and cleanup_job != always.
463 B
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.
238 B
Update from galaxy-dist
63 B
File missed in the change set for the re-engineered InstallManager.
68 B
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.
220 B
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.
2.0 KB
Add 2 new sample tracking reports and 2 new workflow reports, each of which provides the total number of items per month and the total number of items per user ( per month ). Clean up the styles in the admin menu and reports menu mako templates. Clarify in the reports config that reports do not support sqlite. Render the samples checkbox ( when editing samples ) at the top of the table cell.
2.4 KB
Update from galaxy-dist
160 B
Add a sequencer emulator webapp for demonstration purposes.
3.7 KB
GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time."
153 B
sample tracking data transfer mechanism streamlined.
914 B
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.
1.2 KB
Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.
849 B
Add the framework components to enable creating a functional test framework for the tool shed.
480 B
Create unit test directory with example test. Enable coverage report generation of unit tests (run_unit_tests.sh will automatically add --with-coverage to nosetests call if coverage is on the path, coverage report can than be generated with 'coverage html' and viewed at htmlcov/index.html). Update .hgignore to reflect these changes.
63 B
Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES
101 B
adding setup_rabbitmq.sh script.
55 B
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.
69 B
Add new sample config to point to tools installed from a tool shed and add additional directories for checking/creating at startup.
41 B
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.
20.5 KB
Bowtie moved to toolshed
16.8 KB
Add Bowtie2 wrapper to main's tool conf.
19.2 KB
Starting the Rgenetics deprecation process - removing all rgenetics sections from tool_conf.xml.sample and fastqc update to dance around EBI_SRA download bogus file extensions
3.3 KB
Updated tool data table for loc files
3.2 KB
Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc)
5.0 KB
Backout af20b15f7eda, these changes will be reapplied after tools using the sam_fa_indices data table have been migrated to the Tool Shed in their original state and updated to use the new table format.
2.6 KB
Fix for tool listing with run_functional_tests.sh -list, contributed by Peter Cock.
3.6 KB
Add the threadpool_kill_thread_limit setting to the tool shed's sample configuration file.
219 B
Enhance Galaxy tool initialization to do the following:
31.0 KB
Pull from galaxy-dist
GALAXY
======
http://galaxyproject.org/

The latest information about Galaxy is always available via the Galaxy
website above.

HOW TO START
============
Galaxy requires Python 2.6 or 2.7. To check your python version, run:

% python -V
Python 2.7.3

Start Galaxy:

% sh run.sh

Once Galaxy completes startup, you should be able to view Galaxy in your
browser at:

http://localhost:8080

You may wish to make changes from the default configuration.  This can be done
in the universe_wsgi.ini file.  Tools are configured in tool_conf.xml.  Details
on adding tools can be found on the Galaxy website (linked above).

Not all dependencies are included for the tools provided in the sample
tool_conf.xml.  A full list of external dependencies is available at:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies