galaxy

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T

John Chilton 972a2ee9a4 Rework tool shed's workflow module factory so only tool module needs to be different.

Fixes dataset collection inputs in the tool shed. Furthermore, this will allow all all future non-tool modules to be the same between Galaxy and the Tool Shed as well. May seem hacky - but it is removing duplication and it makes some intuitive sense that only the tool module would need to function differently between Galaxy and the tool shed anyway - input parameters, if statements, stop and review steps, etc... will all likely not depend on tool shed artifacts.

2014-08-13 22:52:59 -04:00

config

Add tool form basics, refactor ui libraries, add alternative tool form template

2014-08-13 13:53:07 -04:00

contrib

Fix check_galaxy for recent framework changes.

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

cron

Create builds.txt from UCSC's Main browser, not Test.

2014-08-01 13:12:58 -04:00

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

IGB can read over https just fine (but won't follow 307 Temporary Redirects). Remove strip_https flag from IGB external display applications.

2014-07-28 16:25:07 -04:00

doc

Remove additional pieces from old genome index system.

2014-07-27 02:48:40 -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

Rework tool shed's workflow module factory so only tool module needs to be different.

2014-08-13 22:52:59 -04:00

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

Migrate tools from the distribution to the tool shed.

2014-07-28 11:58:52 -04:00

static

Add tool form basics, refactor ui libraries, add alternative tool form template

2014-08-13 13:53:07 -04:00

templates

Add tool form basics, refactor ui libraries, add alternative tool form template

2014-08-13 13:53:07 -04:00

test

Add unit test to merely walk through new workflow render module...

2014-08-13 21:36:10 -04:00

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

Remove additional pieces from old genome index system.

2014-07-27 02:48:40 -04:00

tools

Fix more BibTeX problems caught by @peterjc.

2014-08-06 12:36:27 -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

Initial BibTeX/DOI citation support in tools and histories.

2014-07-23 15:43:13 -05:00

.hgtags

Updated tag latest_2014.08.11 for changeset 7e4d21621ce1

2014-08-12 09:58:36 -04:00

buildbot_setup.sh

Remove additional pieces from old genome index system.

2014-07-27 02:48:40 -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

Add sqlite datatype and corresponding dataprovider

2014-07-07 11:16:09 +10:00

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

Update DRMAA Python version in eggs.ini to 0.7.6.

2014-06-16 13:27:38 +00:00

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

Allow Docker destinations to use --volumes-from option.

2014-07-01 07:07:09 -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

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

Small style fix in run_tests.sh.

2014-07-25 10:40:53 -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

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

2013-06-24 09:28:14 -05:00

run.sh

Automatically use a virtualenv in galaxy_root/.venv/ if it exists (a la Pulsar).

2014-07-11 09:58:08 -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

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 references to migrated tools from tool_conf.xml.main

2014-07-28 12:07:07 -04:00

tool_conf.xml.sample

Migrate tools from the distribution to the tool shed.

2014-07-28 11:58:52 -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

Update tool_list.py to indicate the correct tool_conf.xml (not sample)

2014-08-12 11:28:08 -04:00

tool_shed_wsgi.ini.sample

Add the new builds_file_path to the Tool Shed's config.

2014-08-04 09:17:51 -04:00

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

Merged in jmchilton/galaxy-central-fork-1 (pull request #440 )

2014-07-28 13:15:32 -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