galaxy

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

T

Greg Von Kuster 88ec217ad1 1) Add GridOperations to the admin view's data library grid enabling libraries to be deleted if they are not deleted, or undeleted if they are deleted.

2) Add exception handling around displaying a specific data library, displaying an error message if the library cannot be displayed.

2011-01-17 11:30:00 -05:00

contrib

MacOS X daemon launcher:

2010-12-13 13:54:22 +10:00

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

external_service_types

Added a new updater for number of sample datasets. The number of sample datasets now updates automatically.

2011-01-14 15:09:43 -05:00

lib

1) Add GridOperations to the admin view's data library grid enabling libraries to be deleted if they are not deleted, or undeleted if they are deleted.

2011-01-17 11:30:00 -05:00

locale

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

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

scripts

Moving sample state and dataset transfer status update api methods to the samples api controller.

2010-12-20 16:05:08 -05:00

static

Fix type in 4858:459a8b52dc90.

2011-01-17 11:05:59 -05:00

templates

Refactoring of history grid code to better support history switching both with and without panels.

2011-01-16 16:18:20 -05:00

test

Fix for rendering folders select field for a sample - include hte library's root folder in the select field too. Fix for setting the default name of the sample grid layout. Fix sample tracking functional test script.

2011-01-12 16:15:40 -05:00

test-data

Converted several tools to data table style of loc file handling (Bowtie, BWA, Lastz, Megablast, PerM, SRMA). Cleaned up several tool XML files, removing unnecessary None parameters.

2010-11-08 00:10:13 -05:00

tool-data

Added BWA color space wrapper; fixed names of FASTQ test files to indicate data type

2011-01-12 12:13:54 -05:00

tools

Fixed edge case error handling when no matching rs

2011-01-15 21:06:17 +11:00

.hgignore

Ignore backup files from some editors

2010-10-13 11:28:37 +01:00

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

trackster: Add bigWig display to trackster. Automatically converts wig to bigwig if needed (NOTE: datatypes_conf.xml.sample has been edited to add the new converter, you must update datatypes_conf.xml to use it). The converter requires that wigToBigWig be in the PATH, but no other tools are needed to view bigwig files as they are provided by bx_python.

2010-12-10 14:59:43 -05:00

demo_sequencer_wsgi.ini.sample

Add the config for the demo sequencer.

2010-12-10 13:30:24 -05:00

dist-eggs.ini

Add ctypes egg for the drmaa module under Python 2.4.

2010-11-22 12:24:07 -05:00

eggs.ini

Second pass of the transfer manager and deferred jobs runner. Still fairly alpha.

2011-01-11 15:58:17 -05:00

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

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_demo_sequencer.sh

Add a sequencer emulator webapp for demonstration purposes.

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

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

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

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

Add external_service_types_conf.xml.sample to list of configuration files that need to be initialized by setup.sh and run.sh.

2011-01-11 09:40:42 -05:00

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

setup.sh

Add external_service_types_conf.xml.sample to list of configuration files that need to be initialized by setup.sh and run.sh.

2011-01-11 09:40:42 -05:00

tool_conf.xml.main

FIxed the unwanted changes made in the previous commit

2011-01-07 16:19:59 -05:00

tool_conf.xml.sample

Added BWA color space wrapper; fixed names of FASTQ test files to indicate data type

2011-01-12 12:13:54 -05:00

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

Added BWA color space wrapper; fixed names of FASTQ test files to indicate data type

2011-01-12 12:13:54 -05:00

tool_list.py

add test section option

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

transfer_manager.py

Second pass of the transfer manager and deferred jobs runner. Still fairly alpha.

2011-01-11 15:58:17 -05:00

universe_wsgi.ini.sample

Renamed sequencer to external_service and sequencer_type to external_service_type.

2011-01-07 16:12:36 -05:00

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