opensource/galaxy: Data intensive science for everyone. - galaxy - Gitea: Git with a cup of tea

opensource/galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-13 08:51:38 +08:00

T

Carl Eberhard 50bf56a5d4 history panel: comment out console statements; controllers/visualization: remove non-2.5 compliant 'with' statement

2012-11-29 17:43:15 -05:00

Fix check_galaxy for recent framework changes.

2012-11-27 15:57:05 -05:00

Added script to update NCBI builds list, replaced Broad data source with direct URL, cleaned up help text.

2012-08-23 16:36:58 -04:00

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

Refactor GBrowse external display application. Update WormBase with latest builds and to be able to use reference sites.

2012-08-22 12:35:23 -04:00

Pared Sphinx's mock module list down to those that actually get rid of errors at ReadTheDocs.

2012-11-03 10:25:21 -07:00

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

history panel: comment out console statements; controllers/visualization: remove non-2.5 compliant 'with' statement

2012-11-29 17:43:15 -05:00

Modify some string in Mako templetes for complete i18n support.

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

Allow GenomeSpace OpenID provider for log in.

2012-04-13 15:07:07 -04:00

Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.

2012-11-26 10:18:47 -05:00

history panel: comment out console statements; controllers/visualization: remove non-2.5 compliant 'with' statement

2012-11-29 17:43:15 -05:00

history panel: comment out console statements; controllers/visualization: remove non-2.5 compliant 'with' statement

2012-11-29 17:43:15 -05:00

More enhancements for hte tool shed functional test framework.

2012-11-29 14:39:31 -05:00

Remove blast tools and test data from the distribution, update tool_conf.xml.sample to reflect this.

2012-08-22 16:12:59 -04:00

Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.

2012-11-26 10:18:47 -05:00

Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.

2012-11-26 10:18:47 -05:00

.hgignore

Ignore shed_tool_data_table_conf.xml in repository.

2012-11-10 22:50:33 -05:00

buildbot_setup.sh

Add shed_tool_data_table_conf.xml.sample to buildbot_setup.sh.

2012-11-07 21:16:17 -05:00

community_wsgi.ini.sample

Make the directory containing the tool shed's hgweb.config file a setting in the tool shed config.

2012-11-12 15:55:24 -05:00

create_db.sh

Allow command-line creation of initial database

2011-11-18 12:41:27 -08:00

datatypes_conf.xml.sample

Add chromatin interaction datatype to datatypes.conf, fix bug in data chrint data provider, and enable diagonal heat map track.

2012-10-22 13:19:09 -04:00

demo_sequencer_wsgi.ini.sample

Add the config for the demo sequencer.

2010-12-10 13:30:24 -05:00

dist-eggs.ini

Provide mercurial as an egg for tool shed operations.

2012-04-23 13:20:29 -04:00

distributed_object_store_conf.xml.sample

Object Store: Store the backend object store's ID in the database when using the distributed object store.

2012-01-09 10:06:23 -05:00

eggs.ini

Download eggs from Galaxy resources in EC2.

2012-10-26 12:56:23 -04:00

external_service_types_conf.xml.sample

Renamed sequencer to external_service and sequencer_type to external_service_type.

2011-01-07 16:12:36 -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

LICENSE.txt

Spiffy new library browser interface. Also, dim datasets in your

2008-09-10 10:10:13 -04:00

manage_db.sh

Fix for sqlalchemy-migrate scripts so they will function across webapps - galaxy is the default, so no command line changes necessary when migrating the db.

2010-07-20 09:27:14 -04:00

manage_tools.sh

File missed in the change set for the re-engineered InstallManager.

2012-02-28 14:07:20 -05:00

migrated_tools_conf.xml.sample

The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed.

2012-02-28 11:38:08 -05:00

openid_conf.xml.sample

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

README.txt

Update README to display a compatible python version as a result of python -V.

2012-11-19 17:05:34 -05:00

reports_wsgi.ini.sample

Add 2 new sample tracking reports and 2 new workflow reports, each of which provides the total number of items per month and the total number of items per user ( per month ). Clean up the styles in the admin menu and reports menu mako templates. Clarify in the reports config that reports do not support sqlite. Render the samples checkbox ( when editing samples ) at the top of the table cell.

2011-02-14 14:54:07 -05:00

run_community.sh

Framework for the Galaxy Community Space.

2010-04-14 10:20:32 -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

Change new functional test flags to conform more closely to previous command line flags

2012-03-30 09:36:21 -04:00

run_galaxy_listener.sh

sample tracking data transfer mechanism streamlined.

2010-11-07 19:46:59 -05:00

run_reports.sh

Improvements to reports management script (run_reports.sh) to enable managing the reports app from CloudMan. These enhancements are all "optional", the default behavior of run_reports.sh is unchanged.

2012-09-21 22:04:15 -05:00

run_tool_shed_functional_tests.sh

Add the framework components to enable creating a functional test framework for the tool shed.

2012-11-13 13:49:09 -05:00

run_unit_tests.sh

Fix unit tests failing on missing dependencies in job runners

2011-02-16 13:48:14 -05:00

run.sh

Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTableEntries that should have been persisted to the XML file were not being handled correctly.

2012-11-07 16:36:28 -05:00

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

setup_rabbitmq.sh

adding setup_rabbitmq.sh script.

2010-10-27 12:36:56 -04:00

shed_tool_conf.xml.sample

Add new sample config to point to tools installed from a tool shed and add additional directories for checking/creating at startup.

2011-09-06 13:41:06 -04:00

shed_tool_data_table_conf.xml.sample

Maintain entries for Galaxy's ToolDataTableManager acquired from installed tool shed repositrories that contain a valid file named tool_data_table_conf.xmnl.sample in a separate config file name shed_tool_data_table_conf.xml. This will ensure that manual edits to the original tool_data_table_conf.xml will not be munged when Galaxy's tool shed installation process automatically adds entries into the file. This enhancement alos includes a bug fix where ToolDataTableEntries that should have been persisted to the XML file were not being handled correctly.

2012-11-07 16:36:28 -05:00

tool_conf.xml.main

Removed lastz and bowtie from tool_conf.xml.main

2012-11-26 10:20:38 -05:00

tool_conf.xml.sample

Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.

2012-11-26 10:18:47 -05:00

tool_data_table_conf.xml.oldlocstyle

Adding data table configuration file for backwards compatibility with local installs: for people who don't want to update loc file style (changes made in rev 4550:535d276c92bc)

2010-11-17 11:32:45 -05:00

tool_data_table_conf.xml.sample

Migrated lastz and bowtie tools to the tool shed. Added a target_file feature to the tool dependency installation process.

2012-11-26 10:18:47 -05:00

tool_list.py

minor whitespace updates, tab/space consistency

2011-07-22 15:17:26 -05:00

tool_sheds_conf.xml.sample

Enhance Galaxy tool initialization to do the following:

2011-09-02 14:57:33 -04:00

universe_wsgi.ini.sample

Add more featureful job limiting and optimize the query for checking whether

2012-11-13 15:00:55 -05:00

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 2.5, 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 universe_wsgi.ini file.  Tools are configured in tool_conf.xml.  Details
on adding tools can be found on the Galaxy website (linked above).

Not all dependencies are included for the tools provided in the sample
tool_conf.xml.  A full list of external dependencies is available at:

http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies