Source code: Difference between revisions

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===CoGe was developed at UC Berkeley and falls under their license which can be read at: http://ipira.berkeley.edu/page.php?nav=41===
==Software licenses==
CoGe was developed has been developed by many people at many universities and has a liberal open source license.  Use as you wish: https://github.com/LyonsLab/coge/commit/ad7eccfd01b9574284bdec31a04639e22bcc6765


==CoGe's Source Code==


CoGe's software is divided into several components:
Available on GitHub: https://github.com/LyonsLab/coge
#Database (mysql)
#Database API (perl)
#Genome Location Visualization: [[GeLo]] (perl)
#Website and applications (perl, javascript, python, flash, HTML)
#Other stuff: alignment algorithms, etc.


== Installation==


As documentation often lags behind development, much of CoGe's software is not in a suitable condition for release. However, once it has been, we will post its code here.  Also, we will be happy to provide any code as requested and do our best to answer any questions you may have about it.
CoGe is a fairly complicated system with many software components (some of which are developed by third parties).


==Download CoGe's genome visualization library [[GeLo]]==
The CoGe team periodically does new installations of the full software stack and tries to keep these installation documents up to date: https://genomevolution.org/wiki/index.php/Install_coge
[[Image:GeLo-example.png|thumb|500px]]
#[[GeLo | CoGePedia page]]
#[http://synteny.cnr.berkeley.edu/CoGe/example/GeLo/example_CoGe_Genome_Browser.tar.gz Tarball]
#[http://synteny.cnr.berkeley.edu/CoGe/example/GeLo/ Example implementation] using the [http://code.google.com/p/genome-browser/downloads/list OpenGenes Genome Browser].

Latest revision as of 15:12, 10 November 2014

Software licenses

CoGe was developed has been developed by many people at many universities and has a liberal open source license. Use as you wish: https://github.com/LyonsLab/coge/commit/ad7eccfd01b9574284bdec31a04639e22bcc6765

CoGe's Source Code

Available on GitHub: https://github.com/LyonsLab/coge

Installation

CoGe is a fairly complicated system with many software components (some of which are developed by third parties).

The CoGe team periodically does new installations of the full software stack and tries to keep these installation documents up to date: https://genomevolution.org/wiki/index.php/Install_coge

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