galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 12:13:33 +08:00

T

Nate Coraor cac730987f Make history purge behavior consistent across all UI paths (always

attempt to stop jobs if the creating job is in the purged history),
previously this was not implemented in the grid history view.

2015-03-12 11:40:25 -04:00

client

UI, history: (in the client) when calling purge on the history model, mark the history as deleted as well

2015-03-11 12:51:54 -04:00

config

Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful)

2015-02-28 12:12:10 -05:00

contrib

Rename universe_wsgi.ini -> galaxy.ini everywhere.

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

cron

Convert everything from elementtree to stdlib xml module.

2015-01-29 16:10:56 -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

Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt ). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).

2015-02-27 15:50:28 -05:00

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

Make history purge behavior consistent across all UI paths (always

2015-03-12 11:40:25 -04:00

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

Add all the necessary dependency requires. Note to self: fix the egg dependency resolution bug so we don't have to dot his.

2015-02-14 10:35:42 -05:00

static

UI, history: (in the client) when calling purge on the history model, mark the history as deleted as well

2015-03-11 12:51:54 -04:00

templates

Sanely size the workflow parameter input boxes (at runtime), tweak formatting a bit.

2015-03-12 10:34:01 -04:00

test

Fix bug in workflows test for implicit connections between steps.

2015-03-03 09:37:30 -05:00

test-data

Remove test data files only used by tool tests.

2015-02-09 21:43:57 -05:00

tool-data

2015-02-27 15:50:28 -05:00

tools

Comment out broken liftOver tests.

2015-02-23 23:09:19 -05:00

.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

.gitignore

Update .gitignore to include run_api_tests.html

2015-03-04 09:27:23 -05:00

.hgignore

Dynamically fetch and cache test-data from git repositories if needed...

2015-02-09 21:43:42 -05:00

.hgtags

Update tag latest_2015.01.13 for changeset d677cb314dcc

2015-02-17 09:00:22 -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

CONTRIBUTING.md

Link to "easiest ways to start" card in CONTRIBUTING.md.

2015-02-08 18:17:10 -05:00

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

Bump SQLAlchemy all the way to 0.9.8

2015-02-16 15:09:42 -05:00

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

requirements.txt

Update requirements.txt for SQLAlchemy 0.9.8 (tip)

2015-02-17 09:26:53 -05:00

rolling_restart.sh

Restore a line deleted by mistake. Thanks John.

2015-02-02 17:30:03 +00:00

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

Source the common startup script for run_tests.sh.

2015-01-11 21:43:13 -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

Merge rolling_restart.sh in run.sh by adding --wait parameter.

2015-02-02 16:08:13 +00:00

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