We've created a Galaxy development mailing list to go along with the Galaxy development site. This mailing list will be used for communicating changes and questions about developing for Galaxy on the Helix Systems. Not everyone is on it, only those who specifically requested for access. If you want to be on the galaxy-dev mailing list, just let me know.
As you all are aware, Galaxy is up and running on Helix (http://galaxy.cit.nih.gov). Please log in and try it out. Most of all, please give us feedback about what works, what doesn't, and what could improve. Some of the tools are configured to run on the Biowulf cluster, most run locally.
We also have a separate Galaxy development site (http://galaxy-dev.cit.nih.gov). This is mainly for developing new XML interfaces (so-called tools) for other command line applications already installed on Helix and Biowulf. We've added a few people to the galaxy-dev group, which is necessary to make any changes.
The Galaxy development site is located in /data/galaxy/dev, and the XML files are in /data/galaxy/dev/tools. Because any changes to the XML files requires the Galaxy server be restarted, I've created a wrapper executable, init_galaxy. After making changes, on Biowulf type:
rsh p1286 /data/galaxy/devlog/init_galaxy restart
and this will restart the server on the Galaxy development host (p1286). Most importantly, the server logs are kept in /data/galaxy/devlog. These are key to debugging any changes made.
The main configuration file (universe_wsgi.ini), the tool configuration file (tool_conf.xml), and the tool data configuration file (tool_data_table_conf.xml) are write accessible to those in the galaxy_dev group, as these will be necessary to change when new applications are added.
The development server DOES NOT have access to the internet, so uploading files through HTTP and FTP won't work. Downloading data from UCSC or other external sites will also not work. However, you can copy local files from your /home and /data areas on Helix using the Import Helix file tool.
There is a danger of stepping on each other's toes when making changes, so be sure to use this mailing list to let everyone know when you are making changes and restarting the server.
Feel free to use this mailing list to ask questions and state what you did.
Cheers, David Hoover Helix Systems Staff http://helix.nih.gov