galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 00:12:08 +08:00

T

John Chilton 82fe547a93 First crack at a CONTRIBUTING file for galaxy-central.

Ideally this would come in through a pull request but I am trying to rush through documentation related to Galaxy development ahead of a GSOC application - by all means I would encourage comments related to this commit as well as well as direct modifications.

CONTRIBUTING files are meant to encourge developers to contribute to open source projects by spelling out how to contribute and what is expected from contributions. More resources related to CONTRIBUTION files include:

 - http://contribute.md/
 - https://github.com/blog/1184-contributing-guidelines

This isn't coming at the expense of wiki documentation - I have already made dozens of enhancements to the Develop section of the wiki today and I am planning a huge walkthrough of how to contribute and learn about various aspect of the broader Galaxy community from a new developer perspective. Having this file in place though I feel is an important part of that however.

2015-02-08 15:02:54 -05:00

client

Ui: Use placeholder title

2015-02-06 23:32:58 -05:00

config

Ui: Fix class name

2015-02-06 11:23:19 -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

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 running tool tests for recent control reworking.

2015-02-07 19:32:16 -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

Add script to update the paths to tool config files in installed repositories' metadata.

2015-01-30 12:17:01 -05:00

static

Ui: Use placeholder title

2015-02-06 23:32:58 -05:00

templates

API, configuration: expand exposed settings to include those needed by the masthead in galaxy.masthead.mako, add serializers for config

2015-02-06 13:38:53 -05:00

test

adding a comment and moving out of else statement

2015-02-06 11:05:04 -06:00

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

Merged in dan/galaxy-central-prs (pull request #643 )

2015-02-02 12:04:23 -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

.hgignore

Update hgignore to include all .lock, .pid, and .log files.

2015-02-04 12:07:01 -05:00

.hgtags

Update tag latest_2015.01.13 for changeset 4039bfd5584a

2015-01-21 16:00:24 -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

First crack at a CONTRIBUTING file for galaxy-central.

2015-02-08 15:02:54 -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

Remove GeneTrack tag from eggs.ini as well.

2015-02-02 13:42:29 -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

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