galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 12:13:33 +08:00

T

John Chilton 9ca839fca8 More reworking of job logging.

Drop now duplicated log message in drmaa, condor, cli, etc.... Have local job runner report which job script it is running - but log it as a job script. For each job runner log the full command-line which includes dependency resolution and not the base version produced directly by the tool and use the old format from the external runners.

2014-05-19 11:02:59 -05:00

config

Charts: Fix resizing

2014-05-17 10:45:14 -04:00

contrib

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cron

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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

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lib

More reworking of job logging.

2014-05-19 11:02:59 -05:00

locale

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openid

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scripts

Enhance the galaxy API for the Tool Shed to retrieve the latest installable revision from the Tool Shed from an installed repository, specifying a name and owner. Enhance the ~/scripts/api/install_tool_shed_repositories.py script to allow the changeset_revision to be optional, and if not specified, the latest installable revision will be installed for the repository specified by the name and owner.

2014-05-14 18:13:33 -04:00

static

data libraries: permissions UI and API work, library router fixes, security addition for retrieving paginated roles for given dataset

2014-05-16 18:13:26 -04:00

templates

Allow 'Copy Datasets' page to copy collections as well.

2014-05-15 12:04:58 -05:00

test

Merged in jmchilton/galaxy-central-fork-1 (pull request #384 )

2014-05-18 21:12:36 -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 46 tools from the distribution to the tool shed: gatk, gops, regional variation.

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

tools

Fixes for genomespace exporter recieving UnvalidatedValue objects.

2014-05-19 10:17:36 -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

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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

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

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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

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

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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

Add a config option for controlling the AMQP consumer timeout, catch socket.error and attempt to recover from it.

2014-05-14 16:34:15 -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

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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

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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

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run_tool_shed.sh

I meant to make this file a .sample file.

2014-05-17 10:10:23 -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

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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.

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

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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

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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