EMBOSS: Project Meeting (Mon 10th January 11)
Alan suggested contacting Alan Irwin of the plplot project about the source code for the 4.99j library release we first included in EMBOSS to help track the changes we made.
A new configuration file emboss.standard is installed for all users with a standard set of databases (EDAM, DRCAT and TAX), a standard set of resource definitions for finding these and other databases, and a standard set of server definitions.
Server definitions describe a server which has attributes passed on to all databases, and a cachefile describing each database available from the server. The cachefile is in two locations, one system-wide (with emboss.standard in the share/EMBOSS install directory) and the other in the user's ~/.embossdata directory. Both versions are timestamped, with the most recent copy having priority.
Sets of new applications use EDAM, DRCAT and TAX, including a set of woss* applications to search for EMBOSS applications by EDAM annotation, and a set of drfind* applications to search DRCAT by EDAM annotation, and a set of edam* applications to search EDAM by specific namespaces. A set of onto* applications can also search EDAM and other OBO ontologies.
New ACD datatypes obo, resource and taxon and their output equivalents allow retrieval of entries from these new standard databases.
A new ACD datatype text allows retrieval from a general text database, using any text-based access method that returns an open file. SRSWWW and other methods will need to retrieve single text entries to support this as there is no parser to separate multiple entries in one open file.
It was agreed that the files should be deleted and some other way to handle them should be found. Options include the user generating the files as a post-install step, and distributing them by some other method such as rsync for developers.
Alan and Peter will look into possible ways to reduce the sizes of the index files.
The EMBOSS machines were shut down with the computer room shut down over the weekend but are not available this morning. Alan has contacted the systems group. A manual backup was done at 15:30 just before the shutdown.
The first author will be responsible for reviewing each of the books.