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 2026-09-24 16:30:27 +08:00

T

Daniel Blankenberg 4d88ce03de Improve handling of invalid/expired GenomeSpace tokens in GenomeSpace export tool.

2014-04-09 17:24:56 -04:00

Charts: Add libraries

2014-04-07 19:19:42 -04:00

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

removed dataset hash from the bookmark generated urls since they are not needed and make for ugly track names

2014-04-07 16:29:17 -04:00

Remove broken and/or obsolete tools.

2014-01-27 13:58:31 -05:00

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

Metrics API: allow posting of metrics sending to app.trace_logger.log if available

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

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

Fixed JAVA_JAR_PATH for realigner_target_creator.

2014-04-04 10:37:52 -04:00

Remove debugging statements

2014-04-08 14:14:17 -04:00

The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.

2014-04-09 10:11:48 -04:00

The basis of this change set is to provide some fixes to certain Tool Shed functions for supporting changing HTTP protocols over time (ie.e, https <-> http). In doing this, I've refactored several functions and moved most of the Tool Shed <-> Galaxy URL munging functions to the Tool Shed's common_util.py module. Ive renamed the munging functions to clarify what each of them does. Several duplicate functions have been eliminated from the code as well.

2014-04-09 10:11:48 -04:00

Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.

2014-04-01 11:04:32 -04:00

Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.

2014-04-01 11:04:32 -04:00

Improve handling of invalid/expired GenomeSpace tokens in GenomeSpace export tool.

2014-04-09 17:24:56 -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

Rename ucsc_build_sites.txt to .sample.

2014-02-27 16:37:48 -05:00

.hgtags

Added tag release_2014.02.10 for changeset 5e605ed6069f

2014-02-10 13:22:23 -05:00

buildbot_setup.sh

Remove broken and/or obsolete tools.

2014-01-27 13:58:31 -05:00

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

data_manager_conf.xml.sample

First pass at a plugable Data Manager. Data Managers can be defined locally or installed from a Tool Shed. TODO: Display Data Manager information in the Tool Shed. Do not install Data Managers into Tool Panel. Add tests. Write Docs.

2013-02-14 15:13:06 -05:00

datatypes_conf.xml.sample

Use new Bcf class.

2014-03-27 17:19:39 +01:00

demo_sequencer_wsgi.ini.sample

Add the config for the demo sequencer.

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

dist-eggs.ini

Drop old platforms from dist-eggs.ini.

2013-09-23 18:44:47 -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

Add dependency on requests 2.2.1.

2014-03-20 10:43:24 -05:00

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

Fix for splitting with outputs_to_working_directory = True, also rename a dict and method in jobs to refer to hda instead of dataset to avoid (my own) confusion.

2011-11-03 19:03:55 -04:00

install_and_test_tool_shed_repositories.sh

Fixes for the tool shed's install and test framework.

2014-02-11 16:41:03 -05:00

job_conf.xml.sample_advanced

Add documentation for using GALAXY_SLOTS with local runner.

2014-03-14 08:42:10 -05:00

job_conf.xml.sample_basic

Define and implement job destinations, an improved method for defining resources on which Galaxy will run jobs. Functionality is similar to the current system configured via "URLs" in the Galaxy config file, but job concurrency limits on a per-destination basis works (whereas per-URL limits were broken). Sample configs for the new destination system can be found in job_conf.xml.sample_*. Also, renamed ClusterJobRunner to AsynchronousJobRunner, moved worker threads to BaseJobRunner and significantly expanded both of these classes. Updated the tasks, local, lwr, and pbs runners to use destinations, and to inherit from AsynchronousJobRunner, drmaa coming shortly. This should be entirely backwards-compatible, so if you update to this revision and change nothing, your jobs should all still run exactly as they have before. Regardless, it is not recommended that you upgrade your Galaxy instance with jobs running unless you are willing to risk losing those jobs.

2013-02-07 15:31:09 -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

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

object_store_conf.xml.sample

S3/Swift objectstore refactoring.

2013-11-20 14:30:03 -08:00

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

updated wiki;

2014-03-20 21:00:22 +00:00

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_demo_sequencer.sh

Add a sequencer emulator webapp for demonstration purposes.

2010-12-03 11:43:08 -05:00

run_functional_tests.sh

Rework workflow functional testing so isn't tested by default...

2014-01-11 22:40:18 -06:00

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_tool_shed.sh

Rename community_wsgi.ini.sample to be tool_shed_wsgi.ini.sample, run_community.sh to run_tool_shed.sh, and fix references to these files in the code.

2013-03-18 10:24:03 -04:00

run_unit_tests.sh

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

run.sh

Rename ucsc_build_sites.txt to .sample.

2014-02-27 16:37:48 -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_data_manager_conf.xml.sample

First pass at a plugable Data Manager. Data Managers can be defined locally or installed from a Tool Shed. TODO: Display Data Manager information in the Tool Shed. Do not install Data Managers into Tool Panel. Add tests. Write Docs.

2013-02-14 15:13:06 -05:00

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

Remove migrated tools from main's tool conf.

2014-04-01 11:05:31 -04:00

tool_conf.xml.sample

Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.

2014-04-01 11:04:32 -04:00

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

Migrate 46 tools from the distribution to the tool shed: gatk, gops, regional variation.

2014-04-01 11:04:32 -04:00

tool_list.py

Fix for tool listing with run_functional_tests.sh -list, contributed by Peter Cock.

2013-04-15 10:09:51 -04:00

tool_shed_wsgi.ini.sample

Fixes for the tool shed's install and test framework and enhancements to allow a configurable number of test runs to be stored and displayed.

2013-11-27 15:28:03 -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

Disable manage_dependency_relationships by default to improve startup time.

2014-03-28 16:36:47 -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 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:

https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies