galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-16 07:19:13 +08:00

T

Greg Von Kuster ca6ba6e011 Many history-related feature enhancements, some fixes and enhanced functional tests:

- history sharing is now modeled after workflow sharing - fixes ticket # 63.
- all history features pass encoded history ids between requests
- new, empty histories are no longer created when a user logs in, instead their last accessed history is displayed
- some other things I'm forgetting, I'm sure
This commit also includes a fix for remote user authentication where private roles and default permissions were not created for users ( Ross's and Assaf's issues ).
Many functional test enhancements.

2009-06-29 16:30:16 -04:00

cron

Apparently I only committed these fixes to security. Recommit of changeset 2015:7a447128f2cd from security, Make UCSC build update scripts find elementtree properly

2009-01-24 12:13:47 -05:00

database

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

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

lib

2009-06-29 16:30:16 -04:00

locale

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

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

scripts

Add ability to share histories with multiple users, along with bug fixes and more functional test coverage for history features.

2009-06-05 11:15:25 -04:00

static

New packed scripts

2009-06-26 09:22:31 -04:00

templates

2009-06-29 16:30:16 -04:00

test

2009-06-29 16:30:16 -04:00

test-data

Fixes and functional tests for uploading directories of files from both the Admin view and the Libraries view ( requires new config setting ).

2009-06-16 09:55:15 -04:00

tool-data

merging heads

2009-03-26 11:13:13 -04:00

tools

A tiny bug fix for Sort tool - the delimiter is now defaulted to tab.

2009-06-25 15:34:05 -04:00

.hgignore

somehow .hgignore got clobbered between merges, possibly because I initially had mine ignoring itself. Reverted to the one on galaxy-security.

2009-03-11 00:42:33 +00:00

buildbot_setup.sh

Buildbot setup also needs the directory creation glue.

2008-07-14 13:42:57 -04:00

datatypes_conf.xml.sample

Merging Ian's trackster update with current head

2009-06-11 12:20:03 -04:00

dist-eggs.ini

PyTables and GeneTrack eggs. Still need to bundle up pychartdir.

2009-04-29 17:37:22 -04:00

eggs.ini

Eliminate the problematic GeneTrack eggs from eggs.ini.

2009-05-26 14:59:40 -04:00

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

Add new migration script that creates missing indexes and default data on galaxy_user and history_dataset_association tables. Fix the change datatype display in the edit_attributes template. Fix the tool config for main.

2009-04-21 10:26:58 -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

Separate framework and tool environments.

2008-04-11 20:11:21 +00:00

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

Tweaked some of the bugs nate found out of GeneTrack. Also using SHA1 hashes to generate PNG names so that we can sorta file-cache them at no cost. Might as well if they're going to sit there for a day.

2009-01-27 01:51:02 -05:00

tool_conf.xml.main

Add tool config for GrameneMart data source.

2009-05-27 14:19:59 -04:00

tool_conf.xml.sample

Add ability to share histories with multiple users, along with bug fixes and more functional test coverage for history features.

2009-06-05 11:15:25 -04:00

tool_list.py

add test section option

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

universe_wsgi.ini.sample

Fixes and functional tests for uploading directories of files from both the Admin view and the Libraries view ( requires new config setting ).

2009-06-16 09:55:15 -04:00

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