EMBOSS: Project Meeting (Fri 25th February 2005)


RFCGR/HGMP: Alan Bleasby, Jon Ison, Gary Williams,
Lion: Thomas Laurent
EBI: Peter Rice, Lisa Mullan


1. Minutes of the last meeting

Minutes of the meeting of 28th January 2005 are here

2. Software Development

2.1 Database indexing

Alan reported dbxflat is complete. He is now working on dbxfasta.

2.2 Makefile for documentation

There have been problems with the Makefile.am files for the doc/programs files. These were defined with wildcards to avoid build failures caused by inconsistent commits, but this breaks various versions of make.

Alan has written a utility to search for files and generate the Makefile.am files.

2.3 Eprimer3

Thomas reported zero is appearing in help text as a valid response for a list in eprimer3. The ACD file and source code no longer have this option. Peter will check - probably a help attribute that needs to be edited to match the value list.

2.4 Gcc compiler

Alan will test the new gcc version 4 compiler.

2.5 Domainatrix

Jon reported that Waqas is reviewing the past year's code.Four new programs will be added, to generate ligand binding sites, to read a site contact map, and to generate a signature for a full domain or patches for multiple topologies.

2.6 SRS and EMBOSS

Thomas will update then SRS definitions for EMBOSS when the new SRS release is out. The new SRS 8.1 will support EMBOSS 2.9.0.

The current ACD parser will be rewritten, probably in Icarus.

3. Administration

3.1 Release 2.10.0

Alan reported the release is done, and a minor bugfix has been added..

4. Documentation & Training


Peter has submitted an abstract. He offered to take two posters if Jon has research to present.

4.2 Sourceforge website

Gary will look for pages from the old HGMP suite which have not made it over to sourceforge.

5. User queries and answers

Gary's current list reviewed. Most new issues were already answered.

6. AOB

7. Date Of Next Meeting

Next meeting at 9.30 on April 1st, 2005,