galaxy

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T

John Chilton a1bb89802f Fix proxied API tool downloads.

From IRC:

17:22 < kellrott> Any ideas about how to deal with https://github.com/bgruening/docker-galaxy-stable/issues/50 ?
17:22 < mrscribe> Title: Tool downloads are not working · Issue #50 · bgruening/docker-galaxy-stable · GitHub (at
                  github.com)
17:24 < kellrott> I think its from how the tool download function unlinks a file while holding the open file handle
                  ( https://github.com/galaxyproject/galaxy/blob/dev/lib/galaxy/webapps/galaxy/api/tools.py#L208 )
17:24 < mrscribe> Title: galaxy/tools.py at dev · galaxyproject/galaxy · GitHub (at github.com)
17:27 < jmchilton> Have you tried not unlinking that file?
17:28 < jmchilton> If that fixes it I have no problem just leaving the file in temp - Galaxy leaves a lot of stuff
                   in temp anyway
17:46 < kellrott> yep, that does the trick

Closes bgruening/docker-galaxy-stable#50.

2015-03-26 13:48:08 -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

Fix proxied API tool downloads.

2015-03-26 13:48:08 -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

Sanely size the workflow parameter input boxes (at runtime), tweak formatting a bit.

2015-03-12 10:34:01 -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