Citrina
From GMOD
Revision as of 18:43, 25 January 2007 by 165.124.152.78 (Talk)
- Description
- 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.
- Requirements
- 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/)
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 Unices
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.
- Documentation
- FAQ
Quick Start Guide
Citrina User Guide
- Mailing List
- Citrina discussion list
- Contact
- Josh Goodman (jogoodma AT bio DOT indiana DOT edu )
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