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opensource/galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-21 05:45:37 +08:00

T

Daniel Blankenberg 3f78f9a449 Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00

Charts plugin update

2014-06-24 13:38:13 -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

converted tabs to spaces

2014-04-14 16:43:49 -04:00

remove misc files that slipped past hgignore

2014-04-10 22:54:34 -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

Make sure a repository exists before checking its status - thanks to Nicola Soranzo for finding this issue.

2014-06-27 07:06:48 -04:00

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

Fetch eggs after initializing sample files, per John Chilton's comment.

2014-06-13 17:32:51 -04:00

Circster: add config options for min/max values and color.

2014-06-26 10:56:05 -04:00

Add a confirmation page when purging installed repositories and include a fix for purging an installed repository that has a tool version lineage chain.

2014-06-26 13:54:51 -04:00

Merged in jmchilton/galaxy-central-fork-1 (pull request #423 )

2014-06-24 18:54:52 -05:00

Add framework test tool that has both data and data_collection param - with test case.

2014-05-07 15:39:03 -05:00

Migrate 22 tools from the distribution to the tool shed.

2014-05-19 13:01:46 -04:00

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -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

Add job_metrics_conf.xml to .hgignore

2014-06-14 17:44:07 +02:00

.hgtags

Updated tag latest_2014.06.02 for changeset 8a863a311a6c

2014-06-26 09:10:17 -04:00

buildbot_setup.sh

Add ucsc_build_sites.txt.sample to setup_buildbot.sh

2014-06-02 10:27:58 -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

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

converted tabs to spaces

2014-04-14 16:43:49 -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

Update build platforms for dist-scrambling.

2014-04-15 13:32:01 -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

Drop threadframe for heartbeat (its functionality was integrated in sys in Python 2.5...)

2014-06-12 09:51:45 -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

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 about local runner destination option embed_metadata_in_job.

2014-06-25 08:01:52 -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

job_metrics_conf.xml.sample

Implement collectl job instrumentation plugin.

2014-03-26 11:01:46 -05:00

job_resource_params_conf.xml.sample

Mechanism to define site-specific parameters to aid defining job destinations.

2014-06-03 12:48:18 -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

rolling_restart.sh

Fixed typo on regex

2014-05-15 09:48:17 -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

Add options to the shell script wrappers to run the API tests.

2014-04-30 15:43:21 -04:00

run_galaxy_listener.sh

sample tracking data transfer mechanism streamlined.

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

run_reports.sh

Abstract common startup tasks into scripts/common_startup.sh, which used to be copy_sample_files.sh.

2014-06-13 16:39:59 -04:00

run_tests.sh

Add options to the shell script wrappers to run the API tests.

2014-04-30 15:43:21 -04:00

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

Abstract common startup tasks into scripts/common_startup.sh, which used to be copy_sample_files.sh.

2014-06-13 16:39:59 -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

Abstract common startup tasks into scripts/common_startup.sh, which used to be copy_sample_files.sh.

2014-06-13 16:39:59 -04:00

set_metadata.sh

…

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

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -04:00

tool_conf.xml.sample

Re-add InterMine tools removed in 401ee23dcf2f70d4be0e975bb3e00a43ae1dfdd0.

2014-06-27 14:44:55 -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 22 tools from the distribution to the tool shed.

2014-05-19 13:01:46 -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

Fix old wiki links.

2014-04-10 20:00:45 +02:00

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

Another docfix for recent local job runner changes.

2014-06-25 09:11:26 -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 2.6 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