Difference between revisions of "Citrina"
From GMOD
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| + | ==Summary== | ||
| + | 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 [[wp:Ant|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 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. | 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 | + | 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. |
| − | |||
| − | |||
| − | + | ==Documentation== | |
| − | + | ||
| − | + | [[Media:Citrina-userguide.pdf|Citrina-userguide.pdf]] | |
| − | + | ||
| − | |||
| − | |||
| + | ==Downloads== | ||
| + | [http://prdownloads.sourceforge.net/gmod/citrina-0.5.1.tar.gz?download citrina-0.5.1.tar.gz] | ||
| − | + | [http://prdownloads.sourceforge.net/gmod/citrina-0.5.1-src.tar.gz?download citrina-0.5.1-src.tar.gz] | |
| − | + | ||
| + | ==Mailing List== | ||
| − | + | [http://sourceforge.net/mailarchive/forum.php?forum=gmod-citrina Citrina discussion list] | |
| − | + | ||
| − | + | ||
| − | + | ==Contact== | |
| − | + | ||
| − | [http:// | + | [[Josh Goodman]] (jogoodma AT bio DOT indiana DOT edu ) |
| − | + | ||
| − | + | ||
| + | [[Category:GMOD Components]] | ||
Revision as of 17:23, 9 February 2007
Summary
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/) 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.
Documentation
Downloads
Mailing List
Contact
Josh Goodman (jogoodma AT bio DOT indiana DOT edu )
