galaxy

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T

John Chilton 6fee45fbfd Bugfixes for runtime parameter handling in the workflow run form.

The behavior of these forms was modified in PR 433 (https://bitbucket.org/galaxy/galaxy-central/pull-request/433/fix-allow-editing-workflows-on-the-fly-for/diff# - not merged by me :| ) - so that the entire workflow would be submitted as runtime parameters on each submission.

In addition to this causing bugs related to unvalidated parameters https://trello.com/c/72WuZ8mu and other problems with select parameters (e.g. http://dev.list.galaxyproject.org/Workflow-bug-when-loc-entries-are-missing-tc4666875.html) - I just discovered it would also cause the modified value to be submitted even if the user opts to undo the selection of a runtime workflow parameter and restore the previous selection (i.e. the form would show the original value but the new value would be submitted).

This PR restores the previous behavior of giving the submitted form elements a unique name so every value in the workflow is not replaced as part of the submission - fixing the former problem. The new technique also fixes the other problem as well.

2015-04-06 12:29:40 -04:00

client

Merge pull request #37 from martenson/release_15.03

2015-03-25 15:23:17 -04:00

config

Charts: Add data point labels to all nvd3 charts (without this gene expression analysis using scatter plots is not very useful)

2015-02-28 12:12:10 -05:00

contrib

Rename universe_wsgi.ini -> galaxy.ini everywhere.

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

cron

Convert everything from elementtree to stdlib xml module.

2015-01-29 16:10:56 -05:00

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

Have IGV external display application load a set of links for available genomes via a tool data table that reads a URL (http://igv.broadinstitute.org/genomes/genomes.txt ). The manually specified builds links should now be used to add additional builds, or for alias mapping (e.g. hg_g1k_v37-->b37).

2015-02-27 15:50:28 -05:00

doc

updated sphinx documentation: added managers; added new API controllers; cleanup

2014-10-22 17:55:45 -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

Apply @dannon's change from Galaxy to the Tool Shed disabling static

2015-03-30 11:32:30 -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

Add all the necessary dependency requires. Note to self: fix the egg dependency resolution bug so we don't have to dot his.

2015-02-14 10:35:42 -05:00

static

Merge pull request #37 from martenson/release_15.03

2015-03-25 15:23:17 -04:00

templates

Bugfixes for runtime parameter handling in the workflow run form.

2015-04-06 12:29:40 -04:00

test

Relocate the external set_metadata script to the galaxy_utils package.

2015-03-12 13:17:41 -04:00

test-data

Remove test data files only used by tool tests.

2015-02-09 21:43:57 -05:00

tool-data

2015-02-27 15:50:28 -05:00

tools

Comment out broken liftOver tests.

2015-02-23 23:09:19 -05:00

.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

.gitignore

Update .gitignore to include run_api_tests.html

2015-03-04 09:27:23 -05:00

.hgignore

Dynamically fetch and cache test-data from git repositories if needed...

2015-02-09 21:43:42 -05:00

.hgtags

Update tag latest_2015.01.13 for changeset d677cb314dcc

2015-02-17 09:00:22 -05:00

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

CONTRIBUTING.md

Link to "easiest ways to start" card in CONTRIBUTING.md.

2015-02-08 18:17:10 -05:00

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

Bump SQLAlchemy all the way to 0.9.8

2015-02-16 15:09:42 -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

install_and_test_tool_shed_repositories.sh

Enable more verbose errors for install and test framework(?).

2014-11-19 12:42:17 -05:00

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

requirements.txt

Update requirements.txt for SQLAlchemy 0.9.8 (tip)

2015-02-17 09:26:53 -05:00

rolling_restart.sh

Restore a line deleted by mistake. Thanks John.

2015-02-02 17:30:03 +00:00

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

typo

2014-11-04 13:58:42 -05:00

run_tests.sh

Source the common startup script for run_tests.sh.

2015-01-11 21:43:13 -05:00

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

Merge rolling_restart.sh in run.sh by adding --wait parameter.

2015-02-02 16:08:13 +00:00

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