galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00

T

John Chilton 482e0ce0fa Introduce ToolPanel abtraction.

There are some repeated operations on an odict in Toolbox that could be cleaned up (fewer lines of code, more readable) with new abstraction in place. Starting with __add_tool_to_tool_panel but will work its way to other methods in Toolbox eventually.

Abstraction reduces cyclomatic complexity of Toolbox.__add_tool_to_tool_panel from 23 down to 18.

2014-12-31 18:21:10 -05:00

client

Add classic hidden_data field to tool form

2014-12-29 14:08:35 -05:00

config

Move galaxy.tools.filters to galaxy.tools.toolbox.filters.

2014-12-29 23:07:01 -05:00

contrib

Rename universe_wsgi.ini -> galaxy.ini everywhere.

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

cron

Delete *ancient* cron/cleanup_datsets.py content, but leave a nice deprecation warning and pointer for those who might actually be using it in cron jobs.

2014-12-17 11:00:29 -05:00

database

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

doc

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

lib

Introduce ToolPanel abtraction.

2014-12-31 18:21:10 -05:00

locale

Modify some string in Mako templetes for complete i18n support.

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

openid

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

scripts

Allow specification of multiple data manager configuration files...

2014-12-15 00:20:35 -05:00

static

Add classic hidden_data field to tool form

2014-12-29 14:08:35 -05:00

templates

Bugfix: Apply tool panel filtering in workflow editor.

2014-12-29 11:48:38 -05:00

test

Allow multiple tools with the same id in ToolBox.

2014-12-31 18:21:10 -05:00

test-data

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

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

tool-data

Removed blastdb_p.loc.sample, moved to tool-shed repo

2014-12-10 12:43:33 -05:00

tools

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 7086b87d83a9

2014-12-16 09:00:19 -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

Add --no_cleanup option to tests.

2014-12-27 17:49:16 -05:00

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