galaxy

Data intensive biology for everyone.

https://gitlab.com/einonm/galaxy

Repository

Data intensive biology for everyone.

README.rst

.. 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/ `__

.. image:: https://img.shields.io/badge/questions-galaxy%20biostar-blue.svg
    :target: https://biostar.usegalaxy.org

.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
    :target: https://webchat.freenode.net/?channels=galaxyproject

.. image:: https://readthedocs.org/projects/galaxy/badge/?version=master
    :target: http://galaxy.readthedocs.org/en/master/
    :alt: Documentation Status

.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
    :target: https://travis-ci.org/galaxyproject/galaxy

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 `__ and viewed on the `Galaxy
Trello Board `__.


Galaxy Development
==================

Galaxy welcomes new development! There is extensive documentation on developing
with Galaxy on the `wiki `__.

Source Repository
-----------------

Galaxy development has moved to `Github
`__.

**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
`__ on this.

.. code:: console

    $ git remote add upstream https://github.com/galaxyproject/galaxy
    $ git fetch upstream
    $ git checkout dev
    $ git merge upstream/dev

Citation (CITATION)

If you use or extend Galaxy in your published work, please cite each of the
following publications:

- Goecks, J, Nekrutenko, A, Taylor, J and The Galaxy Team. "Galaxy: a
  comprehensive approach for supporting accessible, reproducible, and
  transparent computational research in the life sciences." 
  Genome Biol. 2010 Aug 25;11(8):R86.

- Blankenberg D, Von Kuster G, Coraor N, Ananda G, Lazarus R, Mangan M,
  Nekrutenko A, Taylor J. "Galaxy: a web-based genome analysis tool for
  experimentalists". Current Protocols in Molecular Biology. 
  2010 Jan; Chapter 19:Unit 19.10.1-21.

- Giardine B, Riemer C, Hardison RC, Burhans R, Elnitski L, Shah P, Zhang Y,
  Blankenberg D, Albert I, Taylor J, Miller W, Kent WJ, Nekrutenko A. "Galaxy:
  a platform for interactive large-scale genome analysis." 
  Genome Research. 2005 Oct; 15(10):1451-5.

See also: http://wiki.galaxyproject.org/CitingGalaxy



BibTeX format:

@article{goecks2010galaxy,
  title={Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences},
  author={Goecks, Jeremy and Nekrutenko, Anton and Taylor, James and The Galaxy Team},
  journal={Genome Biol},
  volume={11},
  number={8},
  pages={R86},
  year={2010}
}

@article{blankenberg2010galaxy,
  title={Galaxy: A Web-Based Genome Analysis Tool for Experimentalists},
  author={Blankenberg, Daniel and Kuster, Gregory Von and Coraor, Nathaniel and Ananda, Guruprasad and Lazarus, Ross and Mangan, Mary and Nekrutenko, Anton and Taylor, James},
  journal={Current protocols in molecular biology},
  pages={19--10},
  year={2010},
  publisher={John Wiley \& Sons, Inc.}
}

@article{giardine2005galaxy,
  title={Galaxy: a platform for interactive large-scale genome analysis},
  author={Giardine, Belinda and Riemer, Cathy and Hardison, Ross C and Burhans, Richard and Elnitski, Laura and Shah, Prachi and Zhang, Yi and Blankenberg, Daniel and Albert, Istvan and Taylor, James and Miller, Webb C and Kent, W James and Nekrutenko, Anton},
  journal={Genome research},
  volume={15},
  number={10},
  pages={1451--1455},
  year={2005},
  publisher={Cold Spring Harbor Lab}
}