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John Chilton
413f476520
See http://singularity.lbl.gov/ for more information on Singularity and see job_conf.xml.sample_advanced for information on setting up job runners to exploit singularity. The biggest current caveat is probably that currently these container images need to be setup manually by the admin and the paths hard-coded for each tool in job_conf.xml. There are people who do such manual setups for Docker (https://github.com/phnmnl/container-galaxy-k8s-runtime/blob/develop/config/job_conf.xml) - so it wouldn't be surprising if someone wanted to set this up for singularity as well. That said I'm sure this will be followed up by magic to fetch and convert Docker containers and leverage published singularity containers (such as mulled can now produce (https://github.com/galaxyproject/galaxy-lib/pull/64).
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy is available via `https://galaxyproject.org/ <https://galaxyproject.org/>`__
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Galaxy Quickstart
=================
Galaxy requires Python 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://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/
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 <CONTRIBUTING.md>`_ .
Roadmap
=============================
Interested in the next steps for Galaxy? Take a look here: https://github.com/galaxyproject/galaxy/issues/1928