galaxy

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

T

Daniel Blankenberg 2469bc7868 Fix for Integer/FloatToolParameter.get_html_field() when 'value' is provided as an integer/float.

Fixes an issue seen when saving workflows: If an integer or float tool parameter is changed to a value of 0 or 0.0 and saved, the form field would be redisplayed using the default tool value; and not the value that is now saved in the database.

2010-10-15 14:30:14 -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

Add support for displaying BAM files at Ensembl

2010-10-06 11:03:28 -04:00

lib

Fix for Integer/FloatToolParameter.get_html_field() when 'value' is provided as an integer/float.

2010-10-15 14:30:14 -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 default file_path to cleanup_datasets.py script. Closes #376

2010-10-07 14:15:19 -04:00

static

trackster:

2010-10-15 14:24:35 -04:00

templates

sample tracking

2010-10-15 08:51:30 -04:00

test

sample tracking functional tests are fixed

2010-10-15 12:49:21 -04:00

test-data

Updated test outputs for pdf/image output tools that differ slightly on updated dependencies.

2010-09-29 17:25:31 -04:00

tool-data

Introduce blastdb_p.loc for protein BLAST databases

2010-09-21 17:05:24 +01:00

tools

Support query anchored and HTML output

2010-10-11 12:31:59 +01:00

.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

New hyphy nj tree test output for ps2pdf version standardized across all systems, and fix for the wig_to_bigwig test.

2010-09-29 23:55:43 -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

Add basic support for bowtie indexes as a datatype (bowtie_base_index, bowtie_color_index), available via datatype conversion. Currently, the indexes need to be converted manually from the FASTA file before use in bowtie, but they can be reused.

2010-10-07 16:59:41 -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

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

Enable 'FASTX-Toolkit for FASTQ data' as a subsection under 'NGS: QC and manipulation' in tool_conf.xml.sample/main.

2010-10-07 09:27:34 -04:00

tool_conf.xml.sample

Adding blastx and tblastx wrappers, tidying

2010-09-28 16:42:53 +01:00

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