galaxy

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

T

Greg Von Kuster 43f98b1969 1) Enhance the InstallManager to provide the installer the ability to choose to install tool dependenceis (or not) rather than automatically installing them.

2) Persist changes to the tool_data_table_conf.xml file only if within the Galaxy webapp.
3) Apply the 1-liner fix from change set 9ffef0de07f5 in Peter van Heusden's pull request which fixes a problem where the __init__ tests if config.database_connection is None.

2012-06-01 14:51:41 -04:00

contrib

Provide a modified check_galaxy.py that is suitable for use with nagios.

2012-05-26 15:00:36 -04:00

cron

Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds

2011-03-29 13:59:07 -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

Adding IGB files.

2012-04-19 12:35:44 -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

1) Enhance the InstallManager to provide the installer the ability to choose to install tool dependenceis (or not) rather than automatically installing them.

2012-06-01 14:51:41 -04:00

locale

Modify some string in Mako templetes for complete i18n support.

2011-11-24 23:56:36 +08:00

openid

Allow GenomeSpace OpenID provider for log in.

2012-04-13 15:07:07 -04:00

scripts

Add a running_functional_tests config setting.

2012-04-18 16:20:17 -04:00

static

Fix compatibility issue with 9765176c63f7

2012-05-30 18:09:26 -04:00

templates

Use backbone to save trackster visualizations.

2012-05-30 16:37:51 -04:00

test

Fix job manager/handler shutdown, functional tests due to referer -> redirect rename, and check_galaxy script for dataset display -> html table change.

2012-04-16 14:56:24 -04:00

test-data

Eliminate teh emboss 5 functional test output data since it is now available in the emboss_5 repository in the tool shed.

2012-03-21 16:41:45 -04:00

tool-data

Skeleton wrapper for Bowtie2.

2012-04-26 15:28:17 -04:00

tools

Add Bowtie2 preset options to Tophat2 wrapper.

2012-05-31 11:08:24 -04:00

.hgignore

Add CSS build artifacts to .hgignore

2012-03-27 11:06:28 -04:00

buildbot_setup.sh

Potential fix for the buildbot.

2012-02-29 16:27:46 -05:00

community_wsgi.ini.sample

Clarify host string value in community_wsgi.ini.

2012-05-03 14:00:32 -04:00

create_db.sh

Allow command-line creation of initial database

2011-11-18 12:41:27 -08:00

datatypes_conf.xml.sample

Do not use tabix for GFF/GTF because tabix is woefully naive about these data formats.

2012-05-15 10:17:44 -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

Provide mercurial as an egg for tool shed operations.

2012-04-23 13:20:29 -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 ssh egg and fix a requirement for the Tool Shed.

2012-05-24 10:05:55 -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

LICENSE.txt

Spiffy new library browser interface. Also, dim datasets in your

2008-09-10 10:10:13 -04:00

manage_db.sh

Fix for sqlalchemy-migrate scripts so they will function across webapps - galaxy is the default, so no command line changes necessary when migrating the db.

2010-07-20 09:27:14 -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

openid_conf.xml.sample

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

README.txt

Fix Python versions in README.txt

2011-10-25 10:54:17 -04:00

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_community.sh

Framework for the Galaxy Community Space.

2010-04-14 10:20:32 -04:00

run_demo_sequencer.sh

Add a sequencer emulator webapp for demonstration purposes.

2010-12-03 11:43:08 -05:00

run_functional_tests.sh

Change new functional test flags to conform more closely to previous command line flags

2012-03-30 09:36:21 -04:00

run_galaxy_listener.sh

sample tracking data transfer mechanism streamlined.

2010-11-07 19:46:59 -05:00

run_reports.sh

Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES

2010-03-01 15:41:30 -05:00

run_unit_tests.sh

Fix unit tests failing on missing dependencies in job runners

2011-02-16 13:48:14 -05:00

run.sh

Allow for starting/stopping multiple servers directly in run.sh.

2012-04-16 16:26:10 -04:00

set_metadata.sh

Egg support overhaul, introduces a number of fixes to the ABI recognition, better build scripts, a rewrite of the eggs library and eliminition of the need for python -ES

2010-03-01 15:41:30 -05:00

setup_rabbitmq.sh

adding setup_rabbitmq.sh script.

2010-10-27 12:36:56 -04:00

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

tool_conf.xml.main

Moved Genome Diversity tools to toolshed, removed from main tool_conf.

2012-04-16 13:31:02 -04:00

tool_conf.xml.sample

Add Slice BAM by regions tool.

2012-05-02 11:32:19 -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

Skeleton wrapper for Bowtie2.

2012-04-26 15:28:17 -04:00

tool_list.py

minor whitespace updates, tab/space consistency

2011-07-22 15:17:26 -05:00

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

Fix an artifact left over from an incomplete merge

2012-05-23 12:12:13 -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 2.5, 2.6 or 2.7. To check your python version, run:

% python -V
Python 2.4.4

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