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John Chilton
a9e0297e2e
This reverts commit ce90b2da27.
From IRC:
19:01 < g2roboto> [jgoecks] so, about the asynch workflow submission...
19:02 < g2roboto> [jgoecks] ...what happens when there's an error?
19:02 < jmchilton> jgoecks: yes indeed - one of the reasons it is not on by default
19:03 < g2roboto> [jgoecks] hmm, I just updated my dev branch, made no other changes, and it was "on"
19:03 < jmchilton> Big workflow?
19:03 < g2roboto> [jgoecks] yes
19:03 < jmchilton> how many steps?
19:03 < g2roboto> [jgoecks] 43
19:03 < jmchilton> Ah - just over the 40 cutoff
19:03 < jmchilton> I can turn the default back up if you would like
19:04 < g2roboto> [jgoecks] where the threshold? I need to figure out why the workflow is failing, which is my
biggest issue right now
19:04 < jmchilton> we just dropped it from 250 to 40
19:05 < jmchilton> if you want to just change it - I can give you the option , one second
19:05 < jmchilton> force_beta_workflow_scheduled_min_steps=40
19:06 < g2roboto> [jgoecks] If there's no way to show or recover from error, 40 may be too low.
19:06 < jmchilton> yeah - I think you are right
19:06 < jmchilton> clearly - the fact that someone has already hit the problem
19:07 < jmchilton> the long term solution was I think to a invocations into the history panel - but maybe a medium
term solution is just to montior the workflow invocations like tool shed installs... hmm... at
any rate I'll put the default back up
.. figure:: https://wiki.galaxyproject.org/Images/GalaxyLogo?action=AttachFile&do=get&target=galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy is available via `http://galaxyproject.org/ <http://galaxyproject.org/>`__
Galaxy Quickstart
=================
Galaxy requires Python 2.6 or 2.7. To check your python version, run:
.. code:: console
$ python -V
Python 2.7.3
Start Galaxy:
.. code:: console
$ 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
======
Issues can be submitted to trello via the `galaxyproject
website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy
Trello Board <https://trello.com/b/75c1kASa/galaxy-development>`__
Galaxy Development
==================
Galaxy welcomes new development! There is extensive documentation on developing
with Galaxy on the `wiki <https://wiki.galaxyproject.org/Develop>`__.
Source Repository
-----------------
Galaxy development has moved to `Github
<https://github.com/galaxyproject/galaxy>`__.
**Developers** should develop against the ``dev`` branch in the Github
repository.
**Deployers** can continue to pull Galaxy changes from Bitbucket without
interruption. Alternatively, deployers can track the ``master`` branch in
Github.
Syncing a Fork
--------------
If you fork Galaxy to work on it, you may be interested in keeping your copy
up to date with respect to the main repository. Github has `good documentation
<https://help.github.com/articles/syncing-a-fork/>`__ on this.
.. code:: console
$ git remote add upstream https://github.com/galaxyproject/galaxy
$ git fetch upstream
$ git checkout dev
$ git merge upstream/dev