galaxy

mirror of https://github.com/galaxyproject/galaxy.git synced 2026-10-13 08:51:38 +08:00

T

Dave Clements 9d0e631203 Updated "Example" images shown at the bottom of many

"Operate on Genomic Invervals" tool pages.  Old onew were looking dated.
New ones look, well, newer, and cover more cases.

2011-12-19 02:44:31 -08:00

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 UCSC VCF external display application.

2011-12-20 15:40:07 -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

Ensure that the integrated datatypes registry configs exist when needed.

2011-12-20 09:38:15 -05:00

locale

Modify some string in Mako templetes for complete i18n support.

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

scripts

Fix extra files display with object store and the distributed object store config.

2011-12-13 00:45:52 -05:00

static

Updated "Example" images shown at the bottom of many

2011-12-19 02:44:31 -08:00

templates

Don't allow repository names to be changed if the repository has been cloned at least 1 time.

2011-12-20 14:31:13 -05:00

test

Fix for some output changes I made to functional tests.

2011-12-08 10:14:29 -05:00

test-data

Add missing test files

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

tool-data

GATK tools will now use their own .loc file for picard indexes and will also load annotations from an external file.

2011-12-05 12:27:54 -05:00

tools

Updated "Example" images shown at the bottom of many

2011-12-19 02:44:31 -08:00

.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

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

datatypes_conf.xml.sample

Add UCSC VCF external display application.

2011-12-20 15:40:07 -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

Rename HierarchicalObjectStore to DistributedObjectStore.

2011-12-08 17:46:59 -05:00

eggs.ini

Merge galaxy-central

2011-11-15 12:35:57 -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

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 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 VCF viewer for IGV. Add necessary datatypes and converters to support this view (vcf_bgzip; vcf_bgzip to tabix).

2011-11-15 17:24:38 -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 EBI ENA SRA tool contributed by Iain Cleland.

2011-12-13 09:45:49 -05:00

tool_conf.xml.sample

Add Maximal Information-based Nonparametric Exploration (MINE) tool.

2011-12-16 12:54:21 -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_shed_install.xml.sample

Make the tool_shed_install.xml.sample file ready for installing the correct versions of the emboss_5 and emboss_datatypes repositories from the main Galaxy tool shed.

2011-12-20 14:15:39 -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

1. Add a new UpdateManager for use with tool shed repositories installed into a local Galaxy instance. The UpdateManager will poll all appropriate tool sheds to see if updates are available for each of the installed repositories. Polling occurs when the Galaxy server is started. In addition, a config setting tells the UpdateManager to poll after the configured number of hours have passed. If updates are available for an installed repository, a table column is updated, and the repository name is highlighted in red, alerting the Galaxy admin that updates are available for that repository.

2011-12-14 10:18:43 -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