galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-24 16:30:27 +08:00

T

John Chilton 3d9da261d1 Allow tool conf 'tool_path' resolution relative to conf file.

Relative 'tool_path' directories are resolved relative to GALAXY_ROOT (or really working directory). This is probably the expected behavior - but I think it is advantageous to be able to find tools relative to the tool_conf file also. This can now be done using string.Template resolution of ${tool_conf_dir}.

2014-06-23 16:32:24 -05:00

config

Charts: Fix last change

2014-06-20 03:37:10 -04:00

contrib

Fix check_galaxy for recent framework changes.

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

cron

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database

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display_applications

converted tabs to spaces

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

doc

remove misc files that slipped past hgignore

2014-04-10 22:54:34 -05:00

external_service_types

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lib

Allow tool conf 'tool_path' resolution relative to conf file.

2014-06-23 16:32:24 -05:00

locale

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openid

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scripts

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

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

static

Remove debugging from 4d11f59; add packed script

2014-06-18 10:04:10 -04:00

templates

Eliminate the use of the common_install_util module for Galaxy installs from the Tool Shed.

2014-06-18 22:08:00 -04:00

test

Allow tool conf 'tool_path' resolution relative to conf file.

2014-06-23 16:32:24 -05:00

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

Migrate 22 tools from the distribution to the tool shed.

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

tools

Reorder imports post-PR 403.

2014-06-09 10:53:00 -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 9b78595ec114

2014-06-18 08:59:08 -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

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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

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dist-eggs.ini

Update build platforms for dist-scrambling.

2014-04-15 13:32:01 -04:00

distributed_object_store_conf.xml.sample

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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

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extract_dataset_parts.sh

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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

Docfix: Delete diminutive docker doc deficiency.

2014-06-23 12:49:05 -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

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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

updated wiki;

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

reports_wsgi.ini.sample

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rolling_restart.sh

Fixed typo on regex

2014-05-15 09:48:17 -05:00

run_demo_sequencer.sh

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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

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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

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

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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

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shed_tool_data_table_conf.xml.sample

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tool_conf.xml.main

Remove migrated tools from main's tool_conf.xml

2014-05-19 16:38:58 -04:00

tool_conf.xml.sample

Remove migrated tools from the tool conf files.

2014-05-19 13:02:11 -04:00

tool_data_table_conf.xml.oldlocstyle

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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

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universe_wsgi.ini.sample

Update amqp_internal_connection sqlite default in universe_sample to be correct.

2014-06-06 12:08:16 -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