Difference between revisions of "Citrina"
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[[Josh Goodman]] (jogoodma
[[Josh Goodman]] (jogoodma indiana edu )
Revision as of 16:20, 16 January 2008
This project is on hold indefinitely. Over the past couple of years I had hoped to get back to Citrina. However, my other priorities, namely family and work, have left little time for extracurricular coding. Until I find time to revisit this project I suggest you try BioMaj (http://biomaj.genouest.org/). This is a fork of Citrina 0.5.1 and it looks like they have done a nice job tweaking and reinventing it based on the feature list.
Citrina (sih-TREE-nuh) is a database management tool that automates the mirroring and processing of databases that are distributed via ftp servers. It is built around the Ant java build tool making it very flexible and portable. Citrina only provides the basic functionality for mirroring but can easily be extended to do other tasks. For example, with Citrina you could mirror the uniprot database to your local system, generate fasta files, create the blast dbs, and run blast on a set of proteins you are interested in. Or it can be used to transfer Chado SQL dumps between organism sites and automatically populate the postgres database via Ant's SQL tasks. Ant can also execute external scripts so Citrina can take advantage of any existing processing tools that you have already developed.
- Java 1.4.x (http://java.sun.com/j2se/)
- Ant 1.6.x (http://ant.apache.org/)
- Wget 1.6 or higher (http://www.gnu.org/software/wget/wget.html)
- GNU Tar 1.13 or higher (http://www.gnu.org/software/tar/tar.html)
- Gzip 1.3.3 or higher (http://www.gzip.org/) or Bzip2 0.9.0 or higher (http://sources.redhat.com/bzip2/)
Tar, Gzip, and Bzip2 are only needed if you need to extract files that use those compression formats.
Citrina has only been tested on Redhat Linux 9, Solaris 2.8, and SuSe 9.1. Other Unix's including Mac OS X should also work but they have not been tested. It will not run on Windows due to its unique use of symbolic links.
Josh Goodman (jogoodma A*T indiana D*O*T edu )