galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-29 17:42:12 +08:00

T

Martin Cech 7f4e8140a1 propagate the commit of 795336f22d8b94b86256b1d4738ee1bf24e18b57 that is already in next-stable to the stable

original commit msg:
none of the requests & forms controllers used escaping so I escaped the variables exclusively in the templates

2014-12-03 13:29:03 -05:00

client

open citation url in _blank (prevents browser's insecure content error messages while trying to open in the middle pane - https vs http)

2014-11-13 14:41:49 -05:00

config

Charts: Fix selection grid

2014-09-19 13:11:06 -04:00

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

…

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

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -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

Don't escape full strings containing desired html.

2014-12-02 13:50:32 -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

Fix for datatypes consuming output extra files path for the change in d781366.

2014-10-15 12:57:10 -04:00

static

open citation url in _blank (prevents browser's insecure content error messages while trying to open in the middle pane - https vs http)

2014-11-13 14:41:49 -05:00

templates

propagate the commit of 795336f22d8b94b86256b1d4738ee1bf24e18b57 that is already in next-stable to the stable

2014-12-03 13:29:03 -05:00

test

More flexibility for tool data table configuration in the install and test framework.

2014-10-09 14:17:33 -04:00

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

Always access UCSC Main via HTTPS.

2014-09-22 11:31:56 -04:00

.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

Initial BibTeX/DOI citation support in tools and histories.

2014-07-23 15:43:13 -05:00

.hgtags

Update tag latest_2014.10.06 for changeset acb2548443ae

2014-11-27 09:00:14 -05:00

buildbot_setup.sh

Use common_startup.sh for buildbot instead of maintaining a duplicate copy of the samples list.

2014-09-23 10:40:39 -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

Fix another instance of the renaming that I broke.

2014-09-16 18:29:12 -04:00

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

Source virtualenv before python check and for reports app

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

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

…

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