galaxy

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

T

Ross Lazarus 7d2dd59186 Fixes to rgManQQ.py to handle chromosome oddities like 'chr1' and X.

Also cleaned up redundant file recreation - the code passes column numbers to R so the raw data can be read as supplied by Galaxy
Thanks to Alison Harrill for exposing some more input edge cases...

2011-07-20 12:17:43 +10:00

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

Fix LibraryField grouping issue by adding prefix

2011-07-19 21:22:07 -04:00

locale

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

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

scripts

Case sensitivity note for login not found error.

2011-07-18 15:02:37 -04:00

static

Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well.

2011-07-18 21:56:23 -04:00

templates

Various tool shed fixes and enhancements:

2011-07-19 11:27:16 -04:00

test

Escaping in tests should be more specific

2011-06-17 16:45:25 -04:00

test-data

Add missing test files

2011-06-10 20:10:09 -04:00

tool-data

Update annotation profiler tool sample configuration file.

2011-07-07 12:13:49 -04:00

tools

Fixes to rgManQQ.py to handle chromosome oddities like 'chr1' and X.

2011-07-20 12:17:43 +10:00

.hgignore

Change many tool shed methods to use the mercurial api. Fix 2 bugs introduced when email alerts were added - unauthenticated users can once again browse categories / repositories.

2011-06-28 10:24:49 -04:00

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

Sniffers: Fix sniffers not being loaded from datatypes.conf file. Modify VCF sniffer to just check a simple header string.

2011-06-14 13:22:12 -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

Testing Python 2.7.

2011-06-08 23:50:07 -04:00

eggs.ini

Upgrade to Mako 0.4.1 and fix failing tests due to entity escaping. Improve error message for checking strings in history.

2011-06-17 15:23:28 -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

Remove hardcoding of universe_wsgi.ini, fixes issue #358 (except for the sample cleanup scripts which, as samples, are expected to be modified by the site anyway).

2011-06-08 12:10:51 -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_rabbitmq.sh

adding setup_rabbitmq.sh script.

2010-10-27 12:36:56 -04:00

tool_conf.xml.main

Add Genome Diversity tools to Main

2011-06-16 09:54:30 -04:00

tool_conf.xml.sample

Backed out changeset 48bbe32beefe which introduced a whole bunch of unintended reversions from a broken hg repository

2011-07-06 09:44:56 +10:00

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 color-space Tophat wrapper

2011-06-24 16:55:43 -04:00

tool_list.py

add test section option

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

universe_wsgi.ini.sample

Make the ability for users to purge their own data conditional on a config variable. Due to limitations in the grid framework, the button can't be removed from the history grid, but clicking it just does the same thing as delete but adds a message explaining that the purge operation wasn't performed.

2011-06-20 13:43:19 -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