galaxy-beta2

We're live:

https://github.com/natefoo/galaxy-beta2

Science Score: 41.0%

This score indicates how likely this project is to be science-related based on various indicators:

✓
CITATION.cff file
Found CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
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.zenodo.json file
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DOI references
○
Academic publication links
✓
Committers with academic emails
44 of 104 committers (42.3%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (11.0%) to scientific vocabulary

Keywords from Contributors

cloudman usegalaxy bioinformatics cwl workflows common-workflow-language commonwl sciworkflows genomics gtk

Last synced: 10 months ago · JSON representation ·

Repository

We're live:

Basic Info

Host: GitHub
Owner: natefoo
License: other
Language: Python
Default Branch: dev
Homepage: https://github.com/galaxyproject/galaxy
Size: 54 MB

Statistics

Stars: 0
Watchers: 2
Forks: 1
Open Issues: 0
Releases: 0

Created over 11 years ago · Last pushed almost 6 years ago

Metadata Files

Readme Contributing License Citation

README.rst

.. figure:: https://wiki.galaxyproject.org/Images/Logos?action=AttachFile&do=get&target=galaxyLogoTrimmed.png
   :alt: Galaxy Logo

The latest information about Galaxy is always available via the Galaxy
website: `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 `__ and viewed on the `Galaxy
Trello Board `__


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

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

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

Owner

Name: Nate Coraor
Login: natefoo
Kind: user
Location: State College, PA
Company: @galaxyproject

Repositories: 97
Profile: https://github.com/natefoo

System Administrator, Programmer, Whatever else

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}
}

GitHub Events

Total

Last Year

Committers

Last synced: 12 months ago

All Time

Total Commits: 14,664
Total Committers: 104
Avg Commits per committer: 141.0
Development Distribution Score (DDS): 0.847

Past Year

Commits: 0
Committers: 0
Avg Commits per committer: 0.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
Greg Von Kuster	g**g@b**u	2,249
Jeremy Goecks	j**s@e**u	1,514
John Chilton	j**n@g**m	1,514
Daniel Blankenberg	d**n@b**u	1,451
Nate Coraor	n**e@b**u	1,170
Dannon Baker	d**r@g**m	960
James Taylor	j**s@j**g	732
Carl Eberhard	c**d@g**m	732
Aysam Guerler	a**r@g**m	619
Dave Bouvier	d**e@b**u	612
Kanwei Li	k**i@g**m	380
Ramkrishna Chakrabarty	rc@b****u	267
Martin Cech	c**n@g**m	249
Ross Lazarus	r**s@g**m	213
Guruprasad Anada	g**0@b**u	178
Anton Nekrutenko	a**n@b**u	177
Kelly Vincent	k**t@b**u	158
Eric Rasche	r**c@y**u	132
Jeremy Goecks	j**s@g**u	124
Bjoern Gruening	b**g@g**m	117
Peter Cock	p**k@g**m	93
Wen-Yu Chung	w**g@b**u	89
Kyle Ellrott	k**t@g**m	89
Jianbin He	j**e@b**u	88
Ian Schenck	i**n@b**u	86
Nicola Soranzo	s**o@c**t	79
Enis Afgan	a**e@g**m	76
Kyle Ellrott	k**t@s**u	60
Richard Burhans	b**s@b**u	59
Scott McManus	s**s@g**u	36
and 74 more...

Committer Domains (Top 20 + Academic)

bx.psu.edu: 20 emory.edu: 3 crs4.it: 3 uncc.edu: 2 nbic.nl: 2 msi.umn.edu: 2 well.com: 1 bu.edu: 1 plantandfood.co.nz: 1 50mail.com: 1 cs.man.ac.uk: 1 umn.edu: 1 princeton.edu: 1 illumina.com: 1 galaxyproject.org: 1 gatech.edu: 1 soe.ucsc.edu: 1 unimelb.edu.au: 1 gwu.edu: 1 yandex.ru: 1 uwaterloo.ca: 1 sanbi.ac.za: 1 uci.edu: 1 uga.edu: 1 cs.wisc.edu: 1 alum.mit.edu: 1 mit.edu: 1 vbi.vt.edu: 1 louisville.edu: 1

Issues and Pull Requests

Last synced: 12 months ago

All Time

Total issues: 1
Total pull requests: 1
Average time to close issues: 6 days
Average time to close pull requests: over 1 year
Total issue authors: 1
Total pull request authors: 1
Average comments per issue: 10.0
Average comments per pull request: 0.0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 0
Average time to close issues: N/A
Average time to close pull requests: N/A
Issue authors: 0
Pull request authors: 0
Average comments per issue: 0
Average comments per pull request: 0
Merged pull requests: 0
Bot issues: 0
Bot pull requests: 0

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Applications

Experiments

Open Source Science

galaxy-beta2

Science Score: 41.0%

Keywords from Contributors

Repository

Basic Info

Statistics

Metadata Files

README.rst

Owner

Citation (CITATION)

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels