In the wake of the GMOD Summer School a little over a week ago, I decided that I should create a release that has the tools that I used to tie together GBrowse, Apollo and Chado. It can be downloaded at:
These utilities consist of 4 main tools:
- A CGI for selecting a region in GBrowse, extracting the data for
that region from Apollo and creating an XML file and a Java Webstart (.jnlp) file for Apollo.
- A CGI for accepting uploads of edited XML files to either be
immediately loaded into Chado or to be held for validation.
- A configuration perl module to make modifying the CGI's behavior easy.
- A Module::Build based installer that queries the user for needed setup data.
While this release of cas-utils assumes that the port for connecting to the database is blocked for outside users, future releases of these tools could be configured to assume the reverse. Another item planned for a future release is tools for integrating Chado with a MediaWiki site for more text-based annotation. Of course, because of the nature of these tools, it is assumed that several things are already in place and working:
- Chado with computational analysis and annotation data already loaded.
- GBrowse (either 1.69 (to be released soon) or from the stable cvs branch).
- Apollo, both as an installed application (like in /usr/bin), and as
source that has been built into a webstart application and installed for the web server to use.
If you have questions about either cas-utils or any of the prerequisites, please send questions to the most appropriate mailing list:
- Chado: firstname.lastname@example.org
- GBrowse: email@example.com
- Apollo: firstname.lastname@example.org
I've only tested this application on CentOS 4.6 and Ubuntu 8.04, though there is no reason to believe that this wouldn't work on any Linux and probably on MacOS as well. I am considerably less sure that this would work out of the box on Windows, but support for that could probably be in a future release if the demand is there.
Thanks and happy curating! Scott Cain