galaxy

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

T

Eric Rasche 23b4ddc947 Notebook signatures must be unique

Rather than assigning a static notebook signature, this has been replaced with a randomly,
deterministically generated notebook signature. This is currently done off of the dataset's id,
encoded through trans (so it's the unique hash, and not just the number), however this will need to
be exchanged for history_id whenever we have access to that.

2014-10-18 18:38:01 -04:00

client

ToolForm: Improve validation

2014-10-17 14:11:25 -04:00

config

Notebook signatures must be unique

2014-10-18 18:38:01 -04:00

contrib

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

cron

Create builds.txt from UCSC's Main browser, not Test.

2014-08-01 13:12:58 -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

Merged in lance_parsons/galaxy-central-pull-requests/igv-local-dbkey (pull request #488 )

2014-09-12 13:10:52 -04:00

doc

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -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

Parameters: Add validation

2014-10-17 10:03:13 -04:00

locale

Modify some string in Mako templetes for complete i18n support.

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

openid

Abstract OpenID providers to be defined outside of the Python code and to allow customization of actions. See individual examples in openid/ and the list of enabled OpenID providers in openid_conf.xml.sample. Feedback is welcomed.

2012-03-23 13:41:01 -04:00

scripts

Merge stable.

2014-10-17 08:07:24 -04:00

static

ToolForm: Improve validation

2014-10-17 14:11:25 -04:00

templates

ToolForm: Move dictionary building methods from mako to api.

2014-10-16 12:43:39 -04:00

test

History structure: (<root>/history/structure) horizontal layout of job/history DAG separated into components (a work in progress) and associated qunit tests; Job model and list-item; rudimentary js graph library and tests; Qunit: allow import of test-data; minor fixes

2014-10-15 13:11:30 -04:00

test-data

Add framework test tool that has both data and data_collection param - with test case.

2014-05-07 15:39:03 -05:00

tool-data

Remove additional pieces from old genome index system.

2014-07-27 02:48:40 -04:00

tools

Rework pull request #489 memory handling to respect deployer set _JAVA_OPTIONS.

2014-09-22 13:20:49 -04:00

.coveragerc

Create unit test directory with example test. Enable coverage report generation of unit tests (run_unit_tests.sh will automatically add --with-coverage to nosetests call if coverage is on the path, coverage report can than be generated with 'coverage html' and viewed at htmlcov/index.html). Update .hgignore to reflect these changes.

2013-06-24 09:28:14 -05:00

.hgignore

Initial BibTeX/DOI citation support in tools and histories.

2014-07-23 15:43:13 -05:00

.hgtags

Update tag latest_2014.10.06 for changeset e1404e285ccb

2014-10-16 13:00:13 -04:00

buildbot_setup.sh

scripts/common_startup.sh executes fetch_eggs.py correctly.

2014-09-24 16:54:53 -04:00

CITATION

Adding a CITATION file, http://software-carpentry.org/blog/2013/09/introducing-citation-files.html

2013-09-02 15:02:33 -04:00

create_db.sh

Allow command-line creation of initial database

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

dist-eggs.ini

Update build platforms for dist-scrambling.

2014-04-15 13:32:01 -04:00

eggs.ini

Update DRMAA Python version in eggs.ini to 0.7.6.

2014-06-16 13:27:38 +00:00

extract_dataset_parts.sh

Fix for splitting with outputs_to_working_directory = True, also rename a dict and method in jobs to refer to hda instead of dataset to avoid (my own) confusion.

2011-11-03 19:03:55 -04:00

install_and_test_tool_shed_repositories.sh

Fix another instance of the renaming that I broke.

2014-09-16 18:29:12 -04:00

LICENSE.txt

Reindented license text to make it render better at bitbucket.

2013-01-11 16:00:01 -08:00

manage_db.sh

Change community to tool_shed in manage_db.sh notes.

2013-03-13 11:15:07 -04:00

manage_tools.sh

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

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

README.txt

Rename universe_wsgi.ini -> galaxy.ini everywhere.

2014-09-15 16:43:51 -04:00

rolling_restart.sh

Don't create galaxy.ini, just use the sample if galaxy.ini does not exist. Also fix startup when galaxy.ini.sample. Fixes the universe_wsgi.ini skipping problem Dannon found.

2014-09-15 22:12:18 -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

Recreate run_functional_tests.sh as symbolic link to run_tests.sh.

2014-09-09 08:29:45 -04:00

run_reports.sh

Source virtualenv before python check and for reports app

2014-09-04 15:12:04 -04:00

run_tests.sh

Small improvements to JavaScript testing with run_tests.sh.

2014-09-02 12:35:33 -04:00

run_tool_shed.sh

Rename tool_shed_wsgi.ini.sample to tool_shed_wsgi.ini, fix static and other errors I created when moving it to config/ in the first place.

2014-09-16 14:55:38 -04:00

run.sh

Fix a bug with config/galaxy.ini in run.sh

2014-09-16 17:13:17 -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

tool_list.py

Fixes to tool_list.py for legacy configurations and modified tool confs.

2014-09-25 09:00:38 -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 2.6 or 2.7. To check your python version, run:



% python -V

Python 2.7.3



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 config/galaxy.ini file. Tools can be either installed from the Tool Shed

or added manually. For details please see the Galaxy wiki: 



https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial





Not all dependencies are included for the tools provided in the sample

tool_conf.xml. A full list of external dependencies is available at:



https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies