galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-31 02:28:09 +08:00

T

John Chilton 11a0ebd452 Dataset collections - workflows - allow data_collection params.

Extend workflow running, extraction, viewing to allow tools with data_collection parameters.

This is brutally ugly because "isinstance( input, DataToolParameter )" which was already not very Pythonic has been updated to be "isinstance( input, DataToolParameter ) or isinstance( input, DataCollectionToolParameter )". This should all be reworked with an "is_data_parameter" on base ToolParameter.

2014-05-06 08:54:30 -05:00

config

Charts: Fixes for heatmaps

2014-05-05 16:02:16 -04:00

contrib

Fix check_galaxy for recent framework changes.

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

cron

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

database

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display_applications

Manually graft IGB updates to stable, since the old display applications now no longer work properly.

2014-04-16 10:50:23 -04:00

doc

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

lib

Dataset collections - workflows - allow data_collection params.

2014-05-06 08:54:30 -05:00

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

Rework test framework testing and tools.

2014-04-28 11:48:51 -05:00

static

Dataset collections - allow mapping collection params over subcollections.

2014-05-06 08:54:30 -05:00

templates

Dataset collections - workflows - allow data_collection params.

2014-05-06 08:54:30 -05:00

test

Dataset collections - allow mapping collection params over subcollections.

2014-05-06 08:54:30 -05:00

test-data

Moved API tests to live under test/ rather than test/functional/. Removed test for DNAse flanked genes. Added test for UCSC table browser.

2014-04-30 15:35:57 -04:00

tool-data

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

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

tools

Update NGS read simulator to use job working directory.

2014-04-18 13:31:13 -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_2014.04.14 for changeset 9e53251b0b7e

2014-04-14 19:28:10 -04:00

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

Manually graft IGB updates to stable, since the old display applications now no longer work properly.

2014-04-16 10:50:23 -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

Add simplejson back again until 'anyjson' changes are pushed through bioblend.

2014-04-24 11:03:23 -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

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

Fix spelling. Good catch by Nicola.

2014-04-28 09:50:40 -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

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

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

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_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

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

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

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setup_rabbitmq.sh

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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 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

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

Make checking for for migrated tools when starting the Galaxy server a config setting that defaults to True. This setting should generally be False only for development Galaxy environments that are often set up from scratch (with new db, etc) and migrated tools are not needed in the Galaxy tool panel. In those cases where this setting is False, starting a fresh Galaxy instance (with no checking for migrated tools) will be much faster.

2014-04-28 15:35:41 -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