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opensource/galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-16 15:45:04 +08:00

T

Dannon Baker 1cf97e52ac Merge.

2014-11-25 14:27:04 -05:00

ToolForm: More batch mode validation logic

2014-11-24 14:48:09 -05:00

Enable defense against clickjacking out of the box.

2014-11-25 09:59:40 -05:00

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

Hide the GALAXY env variable. This enables us to set it externally and just call the script. Very useful in docker containers.

2014-10-22 13:10:32 +00:00

Add tool search to workflow editor. Also standardize tool panel structure and style so that it is the same in both the main interface and in the workflow editor; workflow editor now uses styles in tool_menu.css as well.

2010-09-20 13:28:16 -04:00

display_applications

Merged in lance_parsons/galaxy-central-pull-requests/igv-local-dbkey (pull request #488 )

2014-09-12 13:10:52 -04:00

updated sphinx documentation: added managers; added new API controllers; cleanup

2014-10-22 17:55:45 -04:00

external_service_types

Fixes for transferring files from external services using the http protocol. Automatic file transfers from Pac Bio SMRT Portal are functional for version 1.1.0.

2011-04-14 16:42:12 -04:00

Merge.

2014-11-25 14:27:04 -05:00

Modify some string in Mako templetes for complete i18n support.

2011-11-24 23:56:36 +08:00

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

Merge stable.

2014-10-17 08:07:24 -04:00

ToolForm: More batch mode validation logic

2014-11-24 14:48:09 -05:00

Sanitize tag output in tagging_common and user.tags_used; protect against closing tags in bootstrapped JSON (http://benalpert.com/2012/08/03/preventing-xss-json.html ); minor fixes

2014-11-25 14:22:08 -05:00

Bug fix for 21e3d69.

2014-11-19 12:42:17 -05:00

Add framework test tool that has both data and data_collection param - with test case.

2014-05-07 15:39:03 -05:00

Remove additional pieces from old genome index system.

2014-07-27 02:48:40 -04:00

Add rpy requirement.

2014-11-14 14:56:28 +00:00

.coveragerc

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.

2013-06-24 09:28:14 -05:00

.hgignore

Implement workflow scheduling 'plugin' framework.

2014-11-13 13:47:38 -05:00

.hgtags

Update tag latest_2014.10.06 for changeset acc8d1e2bc88

2014-11-19 15:00:25 -05:00

buildbot_setup.sh

scripts/common_startup.sh executes fetch_eggs.py correctly.

2014-09-24 16:54:53 -04:00

CITATION

Adding a CITATION file, http://software-carpentry.org/blog/2013/09/introducing-citation-files.html

2013-09-02 15:02:33 -04:00

create_db.sh

Allow command-line creation of initial database

2011-11-18 12:41:27 -08:00

dist-eggs.ini

Update build platforms for dist-scrambling.

2014-04-15 13:32:01 -04:00

eggs.ini

Update DRMAA Python version in eggs.ini to 0.7.6.

2014-06-16 13:27:38 +00:00

extract_dataset_parts.sh

The "How to Cite Galaxy" link was being read from screencasts_url, not citation_url.

2011-11-02 16:39:08 -04:00

install_and_test_tool_shed_repositories.sh

Enable more verbose errors for install and test framework(?).

2014-11-19 12:42:17 -05:00

LICENSE.txt

Reindented license text to make it render better at bitbucket.

2013-01-11 16:00:01 -08:00

manage_db.sh

Change community to tool_shed in manage_db.sh notes.

2013-03-13 11:15:07 -04:00

manage_tools.sh

File missed in the change set for the re-engineered InstallManager.

2012-02-28 14:07:20 -05:00

README.txt

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

rolling_restart.sh

Don't create galaxy.ini, just use the sample if galaxy.ini does not exist. Also fix startup when galaxy.ini.sample. Fixes the universe_wsgi.ini skipping problem Dannon found.

2014-09-15 22:12:18 -04:00

run_demo_sequencer.sh

Add a sequencer emulator webapp for demonstration purposes.

2010-12-03 11:43:08 -05:00

run_functional_tests.sh

Recreate run_functional_tests.sh as symbolic link to run_tests.sh.

2014-09-09 08:29:45 -04:00

run_reports.sh

typo

2014-11-04 13:58:42 -05:00

run_tests.sh

Small improvements to JavaScript testing with run_tests.sh.

2014-09-02 12:35:33 -04:00

run_tool_shed.sh

Rename tool_shed_wsgi.ini.sample to tool_shed_wsgi.ini, fix static and other errors I created when moving it to config/ in the first place.

2014-09-16 14:55:38 -04:00

run.sh

Fix a bug with config/galaxy.ini in run.sh

2014-09-16 17:13:17 -04:00

set_metadata.sh

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

2010-03-01 15:41:30 -05:00

tool_list.py

Fixes to tool_list.py for legacy configurations and modified tool confs.

2014-09-25 09:00:38 -04:00

README.txt

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 config/galaxy.ini file. Tools can be either installed from the Tool Shed

or added manually. For details please see the Galaxy wiki: 



https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial





Not all dependencies are included for the tools provided in the sample

tool_conf.xml. A full list of external dependencies is available at:



https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies