galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-25 00:12:08 +08:00

T

Greg Von Kuster d3e5f3eda9 Fixes for column filtering and sorting problems introduced in change set 4275:

eea6144270bf.  Queries that include table joins cannot guarantee unique column names, so add support to the grid framework for <column>.key values like <TableName>.<ColumnName>.  Enhance the tool shed grids to take advantage of this so that sorting snd filtering on columns is functionally correct.

2010-09-28 13:11:10 -04:00

contrib

add multiprocess.sh example script for running multiple galaxy processes. instructions coming later.

2010-05-20 17:00:12 -04:00

cron

POSIXize/Bournize updateucsc.sh.sample

2009-09-10 17:31:05 -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

Apply patch from Brad Chapman providing support for detecting, uploading and displaying UCSC bigWig and bigBed. Add new functional tests for uploading and detecting bigbed and bigwig formats, and correct and clean up the test_get_data.py functional test script.

2010-08-19 13:58:10 -04:00

lib

Fixes for column filtering and sorting problems introduced in change set 4275:

2010-09-28 13:11:10 -04:00

locale

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

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

scripts

Use a job to export a history to an archive file. Exporting a history is now enabled in the history options panel, but importing a history is not yet a job and remains disabled. When a user exports a history, a link is provided that can be used to retrieve the archive or, in the future, moved to another Galaxy instance.

2010-09-28 11:40:19 -04:00

static

Updates to help text for Human Genome Variation tools and formatHelp.html

2010-09-28 12:38:52 -04:00

templates

Fixes for column filtering and sorting problems introduced in change set 4275:

2010-09-28 13:11:10 -04:00

test

Rewrite the functional tests that cover all Galaxy forms related behavior. Clean up / fix bugs in several sample run request templates. Fix a bug introduced in change set a8cdece11998 which incorrectly generated selected options in a select list in the data library framework.

2010-09-22 16:38:49 -04:00

test-data

Add test for bz2 file upload

2010-09-10 14:17:05 -04:00

tool-data

Fixed sample .loc file for FunDO tool

2010-09-16 15:29:51 -04:00

tools

Updates to help text for Human Genome Variation tools and formatHelp.html

2010-09-28 12:38:52 -04:00

.hgignore

Fixed creation of new tracks, missing template-generated css for trackster, add .DS_Store, *.rej and *.orig to hgignore

2010-07-12 14:59:11 -04:00

buildbot_setup.sh

Add setup of tool-data/shared/jars to the buildbot setup script.

2010-09-02 11:37:26 -04:00

community_datatypes_conf.xml.sample

Galaxy Tool Shed enhancements

2010-07-22 16:43:32 -04:00

community_wsgi.ini.sample

Community upload functionality

2010-04-23 11:30:16 -04:00

datatypes_conf.xml.sample

added svg datatype

2010-08-25 12:27:24 -04:00

dist-eggs.ini

Minor fixes for scrambling and dist-scrambling

2010-08-17 09:29:38 -04:00

eggs.ini

Upgrade simplejson to 2.1.1 w/ C extension speedup

2010-08-17 09:58:47 -04:00

export_history.sh

2010-09-28 11:40:19 -04:00

LICENSE.txt

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

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

Makefile

Remove outdated about.rst/html.

2010-06-30 11:09:14 -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

MANIFEST.in

Moving james-wsgi branch to new trunk.

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

README.txt

Update the README.txt (just an excuse to trigger the bitbucket->buildbot connection since it should be fixed)

2010-08-18 15:13:23 -04:00

reports_wsgi.ini.sample

Enhancements for the reports webapp:

2010-05-28 16:30:16 -04:00

run_community.sh

Framework for the Galaxy Community Space.

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

run_functional_tests.sh

Remove old Lmap from datatypes_conf.xml.sample - now deprecated from genetics.py

2010-03-10 20:59:11 -05:00

run_galaxy_listener.sh

lims:

2010-04-21 10:41:30 -04:00

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

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.sh

Remove builds.txt from source control - use builds.txt.sample instead and copy it over if you don't have one

2010-05-10 12:50:09 -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.sh

Added missing Bowtie color loc file to setup.sh

2010-08-20 11:16:27 -04:00

tool_conf.xml.main

Add the Human Genome Variation tools to main's tool config.

2010-09-27 15:15:04 -04:00

tool_conf.xml.sample

Updates to disease ontology and lps tools

2010-09-15 12:21:37 -04:00

tool_data_table_conf.xml.sample

Add BFAST Mapper tool and wrapper.

2010-08-18 16:52:06 -04:00

tool_list.py

add test section option

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

transfer_datasets.ini.sample

LIMS data transfer:

2010-02-12 14:01:45 -05:00

universe_wsgi.ini.sample

Fix broken wiki link in sample config.

2010-09-21 09:27:57 -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 2.4, 2.5 or 2.6. 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://bitbucket.org/galaxy/galaxy-central/wiki/ToolDependencies