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| ==Software licenses== | | ==Software licenses== |
| CoGe was developed at UC Berkeley and falls under their license which can be read at: http://ipira.berkeley.edu/page.php?nav=41 | | 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 |
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| Individual tools used in CoGe are subject to their own licenses, and are developed independently of CoGe. Read their licenses.
| | ==CoGe's Source Code== |
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| ==CoGe's components==
| | Available on GitHub: https://github.com/LyonsLab/coge |
| CoGe's software is divided into several components:
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| #Database (mysql)
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| #Database API (perl)
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| #Genome Location Visualization: [[GeLo]] (perl)
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| #Website and applications (perl, javascript, python, flash, HTML)
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| #Other stuff: alignment algorithms, etc.
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| 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.
| | == Installation== |
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| ==CoGe's genome visualization library [[GeLo]]==
| | CoGe is a fairly complicated system with many software components (some of which are developed by third parties). |
| [[Image:GeLo-example.png|thumb|500px]]
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| #[[GeLo | CoGePedia page]]
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| #[http://synteny.cnr.berkeley.edu/CoGe/example/GeLo/example_CoGe_Genome_Browser.tar.gz Tarball]
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| #[http://synteny.cnr.berkeley.edu/CoGe/example/GeLo/ Example implementation] using the [http://code.google.com/p/genome-browser/downloads/list OpenGenes Genome Browser].
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| ==NWAlign==
| | 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 |
| nwalign is the implementation of the Needleman-Wunsch algorithm for global sequence alignments that CoGe uses. This very fast and easily parallelized implementation is written and maintained by Brent Pedersen and can be downloaded at: http://pypi.python.org/pypi/nwalign/
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| ==Python tools for DAGChainer==
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| Brent Pedersen has written an extensive library of tools, including a rewrite of DAGChainer's perl front-end, in python. These tools greatly extend the functionality of DAGChainer. For example, an automated way to merge syntenic blocks by recoding output from a DAGChainer run and resubmitting it back to DAGChainer. These tools can be obtained though an svn repository:
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| svn co http://bpbio.googlecode.com/svn/trunk/scripts/dagchainer
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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