galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-24 02:04:04 +08:00

T

- Converted to use numpy, which is included with Galaxy, instead of rpy, which is not.
- Don't simply skip lines if a numeric parameter encounters non-numeric data, return descriptive error with line contents instead
- General refactoring
- Added new comprehensive test, disabled until test framework supports multiple repeat inputs

2011-06-03 16:08:26 -04:00

contrib

MacOS X daemon launcher:

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

cron

Modified add_manual_builds script so that it will include the build in parentheses after the name even if there are no chromosome lengths listed (previously would not because of line break after name); also added a couple of new manual builds

2011-03-29 13:59:07 -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 IGV as an external display application. Contributed by Tobias Wohlfrom.

2011-03-23 09:57:06 -04:00

external_service_types

Fixes for transferring files from external services using the http protocol. Automatic file transfers from Pac Bio SMRT Portal are functional for version 1.1.0.

2011-04-14 16:42:12 -04:00

lib

Move duplicate data type checker methods from sniff and upload into a new ~/datatypes/checkers.py.

2011-06-03 15:36:59 -04:00

locale

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

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

scripts

Eliminate all suport for tool / tool suite archives from the tool shed. Yikes!

2011-06-02 15:18:35 -04:00

static

Make branding not cover header links

2011-05-26 09:50:07 +02:00

templates

Eliminate all suport for tool / tool suite archives from the tool shed. Yikes!

2011-06-02 15:18:35 -04:00

test

Add a "contains" compare type to functional tests. Enables simple checking for substrings in a test output file, on a line-by-line basis. TODO: Enhance to enforce order.

2011-05-10 20:11:52 -04:00

test-data

[Peter Cock] Filtering tool: Only cast used columns. Fix valid lines and skipped info lines. [Kanwei] Add new testcases to test this behavior. Fixes #537 . Fixes #535

2011-05-27 10:47:17 +02:00

tool-data

Added hg_g1k_v37 to manual builds

2011-05-19 15:38:12 -04:00

tools

Grouping tool:

2011-06-03 16:08:26 -04:00

.hgignore

Ignore backup files from some editors

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

buildbot_setup.sh

Add GATK tool-data to buildbot_setup.sh links.

2011-05-12 12:20:52 -04:00

community_wsgi.ini.sample

Eliminate all suport for tool / tool suite archives from the tool shed. Yikes!

2011-06-02 15:18:35 -04:00

datatypes_conf.xml.sample

BLAST: Fix sniffer for some dataset. Closes #567 . Set mimetype to application/xml. Closes #569

2011-06-02 17:36:38 -04:00

demo_sequencer_wsgi.ini.sample

Add the config for the demo sequencer.

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

dist-eggs.ini

Just build on Solaris 10 for sparc. Apologies to anyone running a 9+ year old OS. ;)

2011-04-18 16:41:38 -04:00

eggs.ini

Revert Mako to 0.2.5 since it breaks fn tests

2011-05-02 13:25:11 -04:00

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

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

README.txt

Remove reference to setup.sh which is no longer used.

2011-03-07 10:02:39 -05:00

reports_wsgi.ini.sample

Add 2 new sample tracking reports and 2 new workflow reports, each of which provides the total number of items per month and the total number of items per user ( per month ). Clean up the styles in the admin menu and reports menu mako templates. Clarify in the reports config that reports do not support sqlite. Render the samples checkbox ( when editing samples ) at the top of the table cell.

2011-02-14 14:54:07 -05:00

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

Fix unit tests failing on missing dependencies in job runners

2011-02-16 13:48:14 -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

tool_conf.xml.main

Add Picard and fastqc tools to Main

2011-05-19 10:07:53 -04:00

tool_conf.xml.sample

separated ngs picard tools and removed fastqc wrapper lgpl annotation

2011-05-17 12:52:24 -04:00

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

Fix circular references between Picard and SRMA entries in data tables sample file

2011-04-25 11:10:45 -04:00

tool_list.py

add test section option

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

universe_wsgi.ini.sample

SMTP Authentication support for all places where Galaxy sends mail. Use STARTTLS where available, too.

2011-06-03 11:25:02 -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

Start 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