galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-09-19 10:51:34 +08:00

T

John Chilton ecb256ef46 Adding db_shell.py that can be used to simplify writing command line

scripts against the Galaxy model/database layer or to make use of
Galaxy models in an interactive shell.

2012-03-05 12:11:53 -06:00

contrib

Fedora(/RHEL/SL/CentOS) init script, thanks Brad Chapman!

2011-12-05 14:55:00 -05:00

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 RViewer external display application.

2012-02-17 10:00:42 -05:00

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

Add config option (sanitize_all_html, still enabled by default) to control strict dataset html output sanitization.

2012-03-05 12:00:53 -05:00

locale

Modify some string in Mako templetes for complete i18n support.

2011-11-24 23:56:36 +08:00

scripts

Adding db_shell.py that can be used to simplify writing command line

2012-03-05 12:11:53 -06:00

static

Fix bug in embedded visualization drag-zoom.

2012-03-01 12:19:28 -05:00

templates

Fix custom-build UI bugs.

2012-03-02 14:29:21 -05:00

test

Enhance the process used by objects to retrieve tools from the tools_by_id dictionary. This allows for workflows that were built with tools originally included in the Galaxy distribution but later moved to the tool shed to function correctly if the tools are installed from the tool shed using Galaxy's update manager. In addition, workflows that were built using locally developed and hosted tools, but the tools were included in a tool shed repository, removed from the local instance, and then installed from the tool shed to function correctly. This approach works for the rerun button on history items as well.

2012-01-17 14:31:06 -05:00

test-data

Add missing test files

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

tool-data

Added apiMel3 to manual builds.

2012-02-23 13:38:01 -05:00

tools

Fix for GATK Depth of coverage tool when using advanced GATK options with one or more target interval inputs defined.

2012-03-01 10:11:55 -05:00

.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

Potential fix for the buildbot.

2012-02-29 16:27:46 -05:00

community_wsgi.ini.sample

Remove the old template_path setting from community_wsgi.ini. since it is set incorrecly and not neede anyway.

2011-11-25 09:24:58 -05:00

create_db.sh

Allow command-line creation of initial database

2011-11-18 12:41:27 -08:00

datatypes_conf.xml.sample

Fix missing gatk_report datatype in datatypes_conf.xml.sample.

2012-02-29 10:27:49 -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

Updates for dist-eggs definitions, Python 2.7 for Mac OS X 10.6+ (intel-only) from python.org is now supported.

2011-09-07 12:28:18 -04:00

distributed_object_store_conf.xml.sample

Object Store: Store the backend object store's ID in the database when using the distributed object store.

2012-01-09 10:06:23 -05:00

eggs.ini

boto 2.2.2 - update eggs.ini

2012-02-24 13:58:01 -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

extract_dataset_parts.sh

The "How to Cite Galaxy" link was being read from screencasts_url, not citation_url.

2011-11-02 16:39:08 -04:00

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

manage_tools.sh

File missed in the change set for the re-engineered InstallManager.

2012-02-28 14:07:20 -05:00

migrated_tools_conf.xml.sample

The InstallManager is now a stand-alone appication that attempts to load the tool panel as closely as possible to the way it was loaded before tools were migrated from the Galaxy distribution to the tool shed.

2012-02-28 11:38:08 -05:00

README.txt

Fix Python versions in README.txt

2011-10-25 10:54:17 -04:00

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 spurious export in run functional tests scripts.

2012-01-17 09:24:37 -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

2012-02-28 11:38:08 -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

shed_tool_conf.xml.sample

Add new sample config to point to tools installed from a tool shed and add additional directories for checking/creating at startup.

2011-09-06 13:41:06 -04:00

tool_conf.xml.main

Add cuffmerge tool wrapper and functional test.

2012-02-01 22:36:17 -05:00

tool_conf.xml.sample

Add cuffmerge tool wrapper and functional test.

2012-02-01 22:36:17 -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

Update tool data tables for GATK.

2011-12-05 12:32:02 -05:00

tool_list.py

minor whitespace updates, tab/space consistency

2011-07-22 15:17:26 -05:00

tool_sheds_conf.xml.sample

Enhance Galaxy tool initialization to do the following:

2011-09-02 14:57:33 -04:00

universe_wsgi.ini.sample

Add config option (sanitize_all_html, still enabled by default) to control strict dataset html output sanitization.

2012-03-05 12:00:53 -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 2.5, 2.6 or 2.7. 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://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Dependencies