galaxy

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

T

John Chilton ce54045b20 Fix bug in registry.py requiring the odd relative import of locally defined data type modules.

So many times I helped people get stuff working by telling them to stick the import in this file without ever understanding why the import needed to be there, the answer would appear to be - because there was a bug.

Kanwei Li fixed the same bug in the sniffer code in d7c529f.

Fixing this bug should allow dynamically injecting datatypes (outside context of tool shed) without modifying Galaxy's source - important for OS packages and planemo.

2014-12-13 23:04:00 -05:00

client

ToolForm: Rename public function

2014-12-12 17:38:23 -05:00

config

Ui: Minor style fix, Charts: Repack scripts

2014-12-10 10:51:37 -05:00

contrib

Rename universe_wsgi.ini -> galaxy.ini everywhere.

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

cron

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

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

Fix bug in registry.py requiring the odd relative import of locally defined data type modules.

2014-12-13 23:04:00 -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

Refactoring: Start abstracting XML processing out of Tool and param classes.

2014-12-11 00:26:13 -05:00

static

ToolForm: Rename public function

2014-12-12 17:38:23 -05:00

templates

Merge next-stable changes to default.

2014-12-11 14:20:21 -05:00

test

Improvements to loading help text from tools.

2014-12-13 22:09:51 -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

Remove additional pieces from old genome index system.

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

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 e416697be38e

2014-12-12 09:00:15 -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

Implement structured tool test data.

2014-12-08 00:21:47 -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