EMBOSS: Project Meeting (Feb 1st 1999)


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

1. Matters Arising


2. Progress on Release 0.0.4

AJB has installed the new release at HGMP.

The local CVS tree still needs some work.

CVS access to the Sanger Centre will require user account for anyone authorized to write to the CVS tree. EB has used this for his own projects and for BioPerl.

EB recommended frequent synchronisation with the repository (cvs update) to reduce the number of clashes when more than one author changes the same file. CVS usually resolves these. So far, PR and IL have only found minor problems when both edited, for example, the same header comment.

An alternative security model in CVS uses Kerberos, but this is not favoured.

EB explained the CVS release process, where a release is created as a branch point. Later bug fixes are made to the release branch, and development work can continue on the main branch. These can be merged later.

The BioPerl pages have a guide to CVS, the URL is http://bio.perl.org/UserInfo/CVShelp.html

EB would like to include WISE code in EMBOSS libraries. The libraries are Library GPL so this needs formal permission from EB. Examples would be dynamic programming and comparison matrix code.

To integrate WISE2, EB would look after the code and PR would provide the ACD files.

3. Documentation

TDB is still working on ACD documentation, starting from a partially complete document that PR had available.

4. New applications

Many of the first applications will be to cover function in EGCG. PR will make a list of applications in EGCG to be converted, and will prepare a list of the most widely used EGCG applications at HGMP.

PR is also working on other applications, for example PHYLIP, and will add these to the application documentation pages.

There was discussion about application naming. An earlier proposal to use "seq" as a prefix was concluded to be too confusing in an alphabetical listing. AJB proposed "DAN" as a name for a DNA melting application.

Standardization is also needed for command line qualifier names.

5. Any other Business


6. Next meeting

Next meeting postponed to Monday 15th February, 11:00 am, in the Sanger Centre Informatics meeting room.
Peter Rice, Informatics Division, The Sanger Centre, Wellcome Trust Genome Campus, Hinxton Hall, Cambridge, CB10 1SA, UK.