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| 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 is a long established initiative to get new algorithms for Bioinformatics developed with Java. Some regard it as less of a workhorse for the typical Bioinformatician than BioPerl, but for many applications it is just far better suited. And it has become key to many bioinformatics suites. == Availability == |
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| 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. |
License-wise everything should now be in order. A dependency on a newer-than-in-main libjgrapht fixes biojava to the contrib section. |
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| * bytecode * common-* * junit4 |
* [http://packages.debian.org/source/sid/libbytecode-java bytecode] * [http://packages.debian.org/source/sid/biojava-live biojava] |
Packaging of BioJava
BioJava is a long established initiative to get new algorithms for Bioinformatics developed with Java. Some regard it as less of a workhorse for the typical Bioinformatician than ?BioPerl, but for many applications it is just far better suited. And it has become key to many bioinformatics suites.
Availability
BioJava comes with many subpackages, which are all directly accessible on their 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 - hm, this seems 4+ years old
- biojava-ensj - presumed to be the sources to the famous ensj.jar that have been long abbandoned by the Ensembl developers but is still found to be used e.g. in martj or Taverna. Some confirmation would be nice.
- biojava-exptl/
- biojava-gadfly/
- biojava-html - some former (?) web site, 8 years old
- biojava-jebl - some experimental bits
- 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 - obsolete, went into biojava-ensembl
- ensembl-das - 5 years old Ensembl-DAS plugin set for Dazzle 0.9x
- webservices/
- xdas/
The current effort to bring BioJava to Debian is focused on BioJava-Live and the libraries it needs.
Issues
License-wise everything should now be in order.
A dependency on a newer-than-in-main libjgrapht fixes biojava to the contrib section.
Libraries already in Debian
[http://packages.debian.org/source/sid/libbytecode-java bytecode]
[http://packages.debian.org/source/sid/biojava-live biojava]
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.
- ensj - should be found on pkg-escience in some outdated version
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!