galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 00:12:08 +08:00

T

John Chilton ae34c75c7b Merged in jmchilton/galaxy-central-fork-1 (pull request #270 )

Delay potential problems with fluent logger dependencies until fluent logger used.

2013-12-03 10:39:21 -06:00

config

Scatterplot (plugin version): small fixes, move dataset out of config, namespace hbrs templates

2013-11-19 10:19:22 -05:00

contrib

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cron

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database

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display_applications

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doc

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external_service_types

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lib

Merged in jmchilton/galaxy-central-fork-1 (pull request #270 )

2013-12-03 10:39:21 -06:00

locale

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openid

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scripts

Functional testing of workflows (for Galaxy).

2013-11-21 19:17:13 -06:00

static

UI: Improve masthead, simplify code

2013-12-03 01:42:58 -05:00

templates

UI: Improve masthead, simplify code

2013-12-03 01:42:58 -05:00

test

Merged in jmchilton/galaxy-central-fork-1 (pull request #269 )

2013-12-03 11:12:57 -05:00

test-data

Restore files that were deleted due to a tool migration, but are still used in test/functiona/test_get_data.py.

2013-11-13 10:46:38 -05:00

tool-data

backout -r 10811

2013-10-08 10:56:03 +11:00

tools

merge stable.

2013-11-30 12:47:19 -05:00

.coveragerc

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.hgignore

Add object_store_conf.xml to .hgignore

2013-11-20 17:39:51 -08:00

.hgtags

Added tag release_2013.11.04 for changeset 26f58e05aa10

2013-11-04 15:04:42 -05:00

buildbot_setup.sh

GCC2013 Advanced Tool and Data Source Configuration workshop: "The test framework uses tool_conf.xml.sample for reasons unknown and lost to time."

2013-06-30 10:04:58 -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

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data_manager_conf.xml.sample

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datatypes_conf.xml.sample

Graph datatypes: re-add to conf.sample returning False from all sniffers; the user must now manually change the type

2013-10-17 13:14:11 -04:00

demo_sequencer_wsgi.ini.sample

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dist-eggs.ini

Drop old platforms from dist-eggs.ini.

2013-09-23 18:44:47 -04:00

distributed_object_store_conf.xml.sample

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eggs.ini

Upgrade psycopg2 to 2.5.1 (statically linked to PostgreSQL 9.2.4).

2013-09-23 18:45:58 -04:00

external_service_types_conf.xml.sample

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extract_dataset_parts.sh

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install_and_test_tool_shed_repositories.sh

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job_conf.xml.sample_advanced

Merge latest galaxy-central-lwr changes.

2013-10-21 16:19:14 -05:00

job_conf.xml.sample_basic

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LICENSE.txt

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manage_db.sh

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manage_tools.sh

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migrated_tools_conf.xml.sample

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object_store_conf.xml.sample

S3/Swift objectstore refactoring.

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

openid_conf.xml.sample

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README.txt

Update README.txt to reflect Python 2.5 is no longer supported.

2013-06-24 09:29:46 -05:00

reports_wsgi.ini.sample

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run_demo_sequencer.sh

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run_functional_tests.sh

Functional testing of workflows (for Galaxy).

2013-11-21 19:17:13 -06:00

run_galaxy_listener.sh

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run_reports.sh

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run_tool_shed_functional_tests.sh

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run_tool_shed.sh

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run_unit_tests.sh

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run.sh

backout -r 10811

2013-10-08 10:56:03 +11:00

set_metadata.sh

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setup_rabbitmq.sh

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shed_data_manager_conf.xml.sample

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shed_tool_conf.xml.sample

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shed_tool_data_table_conf.xml.sample

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tool_conf.xml.main

merge stable.

2013-11-30 12:47:19 -05:00

tool_conf.xml.sample

merge stable.

2013-11-30 12:47:19 -05:00

tool_data_table_conf.xml.oldlocstyle

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tool_data_table_conf.xml.sample

Remove sam_fa_indices.loc.sample from tool-data. Update migration xml to the correct revisions of cufflinks repositories.

2013-10-01 15:49:08 -04:00

tool_list.py

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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

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universe_wsgi.ini.sample

Do not allow deployer to use supplied example master_api_key.

2013-11-07 00:45:09 -06:00

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:

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