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| BioJava comes with many subpackages * biojava-live : core of everything * ? * ? |
BioJava comes with many subpackages, which are all directly accessible on their [http://biojava.org/wiki/CVS_to_SVN_Migration subversion tree], see svn list svn://code.open-bio.org/biojava The following subpackages are available, comments are welcome for the priorisation of the Debianisation process. * biojava-acedb/ * biojava-bsane/ * biojava-chado/ * biojava-corba/ * biojava-ensembl/ * biojava-ensj/ * biojava-exptl/ * biojava-gadfly/ * biojava-html/ * biojava-jebl/ * biojava-lims/ * biojava-live - core of all the biojava classes * biojava-paper/ * biojava2-docs/ * bytecode - some fantastic piece of hack, used in biojava-live for instance to implement HMMs efficiently * das-client/ * das-gui/ * dasregistry/ * dazzle - DAS server of genomic data that visualisers like Ensembl can display dynamically * egads-axis/ * ensembl/ * ensembl-das/ * webservices/ * xdas/ |
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| * dazzle - some years old initiative has stalled due to the delay of the BioJava-Live package. The packaging can still be performed with the Debian sources on debian-med or pkg-escience. | |
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| === some good soul please improve on this page - but not you again, Charles, who you are doing too much already and can do more important things instead === | == Community == Whoever finds time to help out with packaging components of BioJava for Debian please go ahead. Also, this page needs some improvements, still - go ahead! == See also == * [http://www.biojava.org BioJava] Homepage ** [http://biojava.org/wiki/CVS_to_SVN_Migration Subversion instructions] ** [http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk Subversion repository] * |
Packaging of BioJava
BioJava is a long lasting initiative to get new algorithms for Bioinformatics developed with the Java language. It is less a workhorse for the typical Bioinformatician than ?BioPerl is but really a tool for development ... admittedly, you can indeed solve many problems with it.
BioJava comes with many subpackages, which are all directly accessible on their [http://biojava.org/wiki/CVS_to_SVN_Migration subversion tree], see
- svn list svn://code.open-bio.org/biojava
The following subpackages are available, comments are welcome for the priorisation of the Debianisation process.
- biojava-acedb/
- biojava-bsane/
- biojava-chado/
- biojava-corba/
- biojava-ensembl/
- biojava-ensj/
- biojava-exptl/
- biojava-gadfly/
- biojava-html/
- biojava-jebl/
- biojava-lims/
- biojava-live - core of all the biojava classes
- biojava-paper/
- biojava2-docs/
- bytecode - some fantastic piece of hack, used in biojava-live for instance to implement HMMs efficiently
- das-client/
- das-gui/
- dasregistry/
- dazzle - DAS server of genomic data that visualisers like Ensembl can display dynamically
- egads-axis/
- ensembl/
- ensembl-das/
- webservices/
- xdas/
The current effort to bring BioJava to Debian is focused on BioJava-Live and the libraries it needs.
Issues
A first submission was rejected in 2007. Upstream has since added a reference to the LGPL license to a file that had previously "all rights reserved", and now everything should be in order - license-wise.
Libraries already in Debian
- bytecode
- common-*
- junit4
Libraries currently being packaged
- libjgrapht-0.7.3: Current issues are with the jgrapht library whose version is unclear. Debian's current installation is of version 0.6.0, which is outdated but currently remains in order to remain compatible with another program. The pkg-java svn has working packages of version 0.7.3, tests with which are pending.
dazzle - some years old initiative has stalled due to the delay of the BioJava-Live package. The packaging can still be performed with the Debian sources on debian-med or pkg-escience.
Community
Whoever finds time to help out with packaging components of BioJava for Debian please go ahead. Also, this page needs some improvements, still - go ahead!
See also
[http://www.biojava.org BioJava] Homepage
* [http://biojava.org/wiki/CVS_to_SVN_Migration Subversion instructions]
* [http://code.open-bio.org/svnweb/index.cgi/biojava/browse/biojava-live/trunk Subversion repository]