EMBOSS: Project Meeting (Jan 25th 1999)


Sanger Centre: Peter Rice, Ian Longden, Richard Bruskiewicz
HGMP: Gary Williams, Alan Bleasby, Sinead O'Leary, Thon de Boer
(Apologies: Mark Faller, Rodrigo Lopez, Heikki Lehvaslaiho, Martin Senger)

1. Matters Arising

PR has invited Richard Bruskiewicz and Ewan Birney from the Sanger Centre. Thure Etzold (EBI/Lion) is in Hinxton one day per week but cannot attend on Mondays.

PR reported that the Sanger systems group are looking into CVS access to Sanger Centre source code for HGMP and others.

2. Progress on Release 0.0.4

IL and PR continue to work on integrating the graphics library. This must be completed before the release can be built.

IL explained that developers need GNU automake and related software. The recommended versions are:

There have been problems using automake on Linux and SGI/Irix. OSF and Solaris are working.

The new build procedure follows GNU standards. A script "make-all-static" is provided to make building the package easier. This builds the PLplot graphics library and then builds the rest of the package.

PR reviewed the changes in release 0.0.4, including new input and oputput sequence formats and new ACD types for menus which are equivalent to radio buttons, checkboxes, pull down lists and selection lists in HTML depending on how many items can be selected. Agreed: AB to install and test the new release at HGMP

3. Documentation

PR has updated the source code documentation and has built SRS databases for both code (EFUNC) and data structures (EDATA).

PR demonstrated the current outline for application documentation. New sections can be easily added as needed, for example output file descriptions and algorithms.

PR stressed the need for developers to start with simple applications and get familiar with the libraries before trying to understand the full detail. PR continues to work on the documentation.

Agreed: More simple overview of data types and library functions needed. PR to work on this.

Agreed: An overview of ACD file syntax is needed. TDB will work on this.

4. Any other Business

Applications should use "-help" to provide the syntax form the ACD file. PR is working on this ("-help" exists but does nothing at present).

5. Next meeting

Monday 1st February, Sanger Centre Informatics meeting room.
Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.