EMBOSS: Project Meeting (Mon 7th December 09)
Mahmut continues to look into wordmatch. It will be possible to keep the existing data structures, with a wrapper structure to improve efficiency.
Mahmut is patching the Jemboss install script. With a new distribution generated from CVS with "make dist" the new script worked. An ant dependency for a different location is used to test for server results (usually in /tmp/soap/emboss). Without ant the java file needs to be changed and reinstalled. For the release, the ant dependency will be replaced by using a property.
A new parser was needed for tab-separated values with empty fields. This can be merged with the parser used for SAM sequence format.
Jon has a small program to update, including updating relation end points. This also checks the syntax of records, and checks for required relations. It is able to edit ID numbers and renumber terms, and is namespace aware when checking for duplicated names.
At the annotation jamboree in Manchester there was clear interest in EDAM and discussions of use cases. There was no prior agreement on how to annotate, so EDAM was especially helpful.
Alan has set up Syed's old machine (emboss17) as an httpd server. All machines should see /shared/www mounted with an html/ directory. The contents are included in the backup procedures.
The server also has a pure, unadulterated Wiki http://emboss17/wiki where we can register.