Fork of Galaxy (http://galaxyproject.org/) attempting to implement the CWL spec.
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.ci Make some files compatible with Python3 Jun 3, 2016
client Implement a subset of the Common Workflow Language Draft 3 tool format. Jun 13, 2016
config [WIP] Implement Expression tools in Galaxy. Jun 13, 2016
contrib Make some files compatible with Python3 Jun 3, 2016
cron Make some files compatible with Python3 Jun 3, 2016
database Add tool search to workflow editor. Also standardize tool panel struc… Sep 20, 2010
display_applications Add Phinch as an external display application. Currently linking to a… Apr 1, 2016
doc minor docs touch May 27, 2016
external_service_types Fixes for transferring files from external services using the http pr… Apr 14, 2011
lib Update cwl processing for recent changes to cwltool and galaxy. Jun 13, 2016
locale Modify some string in Mako templetes for complete i18n support. Nov 24, 2011
openid Allow GenomeSpace OpenID provider for log in. Apr 13, 2012
scripts Make some files compatible with Python3 Jun 3, 2016
static Implement a subset of the Common Workflow Language Draft 3 tool format. Jun 13, 2016
templates Merge branch 'release_16.04' into dev Jun 13, 2016
test-data Merge branch 'release_16.04' into dev Jun 8, 2016
test Implement a subset of the Common Workflow Language Draft 3 tool format. Jun 13, 2016
tool-data Add Phinch as an external display application. Currently linking to a… Apr 1, 2016
tools Make some files compatible with Python3 Jun 3, 2016
.coveragerc Create unit test directory with example test. Enable coverage report … Jun 24, 2013
.gitignore Merge remote-tracking branch 'galaxyproject/dev' into gie-generic Apr 4, 2016
.travis.yml Drop python2.6 (deprecated, will not be supported in 16.04) from test… Feb 23, 2016
CITATION Adding a CITATION file, http://software-carpentry.org/blog/2013/09/in… Sep 2, 2013
CODE_OF_CONDUCT.md Fix typo found by @nsoranzo. Aug 25, 2015
CONTRIBUTING.md doc tox Oct 15, 2015
CONTRIBUTORS.md Update spelling. May 4, 2016
CWL_TODO Implement a subset of the Common Workflow Language Draft 3 tool format. Jun 13, 2016
LICENSE.txt Add list of contributors Jun 15, 2015
Makefile More clarification of release process. May 18, 2016
README.rst Update README to remove 2.6 May 17, 2016
create_db.sh Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Feb 29, 2016
extract_dataset_parts.sh Fix for splitting with outputs_to_working_directory = True, also rena… Nov 3, 2011
manage_db.sh Fix create/manage db scripts to respect GALAXY_VIRTUAL_ENV. Feb 29, 2016
manage_tools.sh Update more scripts to respect GALAXY_VIRTUAL_ENV. Mar 3, 2016
requirements.txt Pin release wheel verisons. pinned-requirements.txt renamed to Jan 13, 2016
rolling_restart.sh Restore a line deleted by mistake. Thanks John. Feb 2, 2015
run.sh Fixing error in run.sh script Mar 21, 2016
run_reports.sh Another fix for virtualenv fixes. Mar 10, 2016
run_tests.sh Allow setting job_conf path for functional tests. Apr 4, 2016
run_tool_shed.sh change run_tool_shed.py to see the file in the correct lcoation Apr 11, 2016
setup.cfg Fix all E731 "errors". Jan 14, 2016
tool_list.py Make some files compatible with Python3 Jun 3, 2016
tox.ini Drop python2.6 (deprecated, will not be supported in 16.04) from test… Feb 23, 2016

README.rst

Galaxy Logo

The latest information about Galaxy is available via https://galaxyproject.org/

Ask a question Chat with us Release Documentation Inspect the test results

Galaxy Quickstart

Galaxy requires Python 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

Issues and Galaxy Development

Please see CONTRIBUTING.md .

Roadmap

Interested in the next steps for Galaxy? Take a look here: https://github.com/galaxyproject/galaxy/issues/1928