galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-21 13:50:20 +08:00

T

Greg Von Kuster e38e78f5e4 Fixes, cleanup and new functional tests for data types and upload:

- moved all supported binary data types to the new binary.py
- changed GeneTrack data type to subclass from Text rather than Binary
- added Sff data type to datatypes_conf.xml.sample
- merged test_sniffinad_and_metadata_settings.py test scritp into test_get_data.py
- added several additional functional test for data types to test_get_data.py
- fixed some bugs in upload.py when uploading binary data types

2009-11-13 14:13:03 -05:00

contrib

Add contributed Debian init script and OS X LaunchDaemon plist from James Casbon, and my Solaris SMF manifest.

2009-10-30 12:41:17 -04:00

cron

POSIXize/Bournize updateucsc.sh.sample

2009-09-10 17:31:05 -04:00

database

Removed tmp and files from svn, now automatically created via run.sh

2007-05-02 19:23:00 +00:00

lib

Fixes, cleanup and new functional tests for data types and upload:

2009-11-13 14:13:03 -05:00

locale

Integrating i18n support provided by Mitsuteru Nakao, Takashi Hatakeyama, and Hideyuki Morita.

2009-03-17 22:46:47 -04:00

scripts

Officially support Python 2.6.

2009-11-13 10:39:15 -05:00

static

Comment out Galaxy tools from page editor until functional.

2009-11-06 19:11:30 -05:00

templates

Fix for issue #210 , redirect to the proper path when the tool executed form is instructed to redirect.

2009-11-11 14:41:32 -05:00

test

Fixes, cleanup and new functional tests for data types and upload:

2009-11-13 14:13:03 -05:00

test-data

Added sff datatype

2009-11-11 17:55:08 -05:00

tool-data

Add Genetrack tools and display site

2009-11-06 14:22:44 -05:00

tools

Fixes, cleanup and new functional tests for data types and upload:

2009-11-13 14:13:03 -05:00

.hgignore

prepare for new trackster

2009-09-21 20:13:20 -04:00

buildbot_setup.sh

Copy the sample universe_wsgi.ini for buildbot so the new eggs code doesn't bomb

2009-11-05 09:29:03 -05:00

datatypes_conf.xml.sample

Fixes, cleanup and new functional tests for data types and upload:

2009-11-13 14:13:03 -05:00

dist-eggs.ini

Add the GeneTrack egg. Also includes some enhancements and cleanup of the eggs/fetch/scramble code.

2009-11-04 12:58:48 -05:00

eggs.ini

Upgrade to an SVN checkout of SQLAlchemy 0.5.x to resolve a race condition in 0.5.6 proper

2009-11-13 10:09:42 -05:00

LICENSE.txt

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

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

Makefile

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

manage_db.sh

Fix security problem with grids. Template should not be passed at call time, it must be passed at configure time.

2009-08-23 12:28:36 -04:00

MANIFEST.in

Moving james-wsgi branch to new trunk.

2006-11-15 16:28:21 +00:00

README.txt

Remove setup.py, update README.txt

2008-05-02 19:42:59 +00:00

reports_wsgi.ini.sample

merging from central

2008-12-18 16:44:34 -05:00

Revision

Revision info

2007-02-08 20:16:16 +00:00

run_functional_tests.sh

New functional test harness. Update to recent nose. No longer rely on nose to manage the embedded web server (this is not done in functional_tests.py). Log page contents to a temporary file on check_page_for_string error.

2009-10-20 13:08:29 -04:00

run_galaxy_listener.sh

Fixed the bash script to reflect the change in the location of galaxy amq listener script

2009-11-04 13:52:13 -05:00

run_reports.sh

Fix for current month's job report.

2008-05-23 14:13:01 +00:00

run_unit_tests.sh

Exclude controllers from unit tests to eliminate the broken genetrack test.

2009-05-05 08:29:23 -04:00

run.sh

Collapsed changeset: Trackster plugged into galaxy with behind-the-scenes indexing of Wiggle, coverage and interval datasets.

2009-03-11 00:29:01 +00:00

set_metadata.sh

Add the ability for metadata to be set in an external process, this requires set_metadata_externally = True in universe_wsgi.ini.

2009-03-03 12:54:06 -05:00

setup_paths.sh

Skip check_eggs.py for buildbot. If fetch_eggs.py succeeded, they're

2008-03-27 19:32:14 +00:00

setup.sh

Added several loc files to setup.sh and buildbot_setup.sh

2009-11-04 13:58:50 -05:00

tool_conf.xml.main

Incorporate latest grid features into managing users, groups and roles from the admin view.

2009-11-09 23:00:55 -05:00

tool_conf.xml.sample

Remove tool conf typo

2009-11-06 14:36:36 -05:00

tool_list.py

add test section option

2007-10-31 19:12:00 +00:00

universe_wsgi.ini.sample

Add Paste#gzip and visualization module options to universe_wsgi.ini.sample

2009-11-10 16:49:05 -05:00

README.txt

GALAXY
======
http://g2.bx.psu.edu/

The latest information about Galaxy is always available via the Galaxy
website above.

HOW TO START
============
Galaxy requires Python 2.4 or 2.5. To check your python version, run:

% python -V
Python 2.4.4

Before starting Galaxy for the first time, please run the setup script:

% sh setup.sh

If setup.sh finishes successfully, you can then proceed to starting 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://g2.trac.bx.psu.edu/wiki/ToolDependencies