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opensource/galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-30 18:13:23 +08:00

T

Eric Rasche aa6a3bec80 Pandoc conversion to rST due to pypi, see #1

2015-02-21 13:29:58 -05:00

UI: Move action menu rendering into list panel, refactor history contents copying

2015-02-17 09:54:36 -05:00

Merged in erasche2/galaxy-central (pull request #570 )

2015-02-17 09:46:09 -05:00

Rename universe_wsgi.ini -> galaxy.ini everywhere.

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

Convert everything from elementtree to stdlib xml module.

2015-01-29 16:10:56 -05:00

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

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

For select tool parameter, when testing input values, raise ValueErrors instead of assert/AssertionErrors, as ValueError are cased to be caught. Fixes errors on rerun, when options have been removed.

2015-02-17 15:17:17 -05:00

Modify some string in Mako templetes for complete i18n support.

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

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

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

UI: Move action menu rendering into list panel, refactor history contents copying

2015-02-17 09:54:36 -05:00

merge

2015-02-17 09:57:18 -05:00

Add --dockerize and --db [postgres|mysql|sqlite] options to run_tests.sh.

2015-02-21 13:29:58 -05:00

Remove test data files only used by tool tests.

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

Comment out igv local external display application link by default, since it is confusing users (most do not have a local igv running).

2015-02-11 20:39:38 +00:00

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

.gitignore

Add .gitignore

2015-02-21 13:29:58 -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

Update CONTRIBUTING

2015-02-21 13:29:58 -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.rst

Pandoc conversion to rST due to pypi, see #1

2015-02-21 13:29:58 -05:00

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

Add --dockerize and --db [postgres|mysql|sqlite] options to run_tests.sh.

2015-02-21 13:29:58 -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.rst

Galaxy
======

.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target=galaxyLogoTrimmed.png
   :alt: Galaxy Logo

   Galaxy Logo
`galaxyproject.org <http://galaxyproject.org/>`__

The latest information about Galaxy is always available via the Galaxy
website above.

Starting Galaxy
---------------

Galaxy requires Python 2.6 or 2.7. To check your python version, run:

.. code:: console

    $ python -V
    Python 2.7.3

Start Galaxy:

.. code:: console

    $ 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

Issues
------

Issues can be submitted to trello via the `galaxyproject
website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy
Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__