EMBOSS: Project Meeting (Aug 23rd 1999)


Sanger Centre: Peter Rice, Richard Bruskiewich
HGMP: Alan Bleasby, Gary Williams, Val Curwen, Mark Faller

1. Matters Arising


2. General progress on release 0.0.4

Peter has fixed the sequence reading memory leaks (there were two separate leaks).

Peter has added a boolean "AND" function to ACD, treating strings as Yes/No values. Michael Schmitz' build problems were caused by a problem in vararg handling in his gcc compiler installation.

Postscript graphics output is still crashing when the graph title is defined.

Peter has permission to reuse code from FASTA for GCG and blast sequence database formats.

Peter is setting up a new closed mailing list emboss-bug@sanger.ac.uk for EMBOSS support.

There are problems when "../filename" appears on the command line.

Rodrigo Lopez has repeated a request for5 database names to be added in GCG style for FASTA format output so that it can be used to build blast databases. SRS depends on the database prefix to parse blast output.

Wildcards are needed for file input, for example seqretall cannot at present handle "*.seq" as input. Peter already has the code for this in the database reading, and will add it to the file reading routines.

The documentation pages on the Web should be completed and bundled into a tar file on the FTP server. Richard is reday to try compiling a PC version of EMBOSS.

After discussions with Alan, the REBASE folk have agreed to distribute their restriction enzyme database in EMBOSS format.

Alan has added a "range" data type to ACD as several programs now use it. The translation application(s) should be converted to use this data type instead of a string for the locations.

Alan has added embread for data files.

New applications from HGMP: syco, chips, prettyseq.

Peter has looked at the new "readseq" but as the code is all in Java it will be difficult to port to C.

3. Preparation for Beta Release

Peter will announce the beta release when the emboss-bug mailing list is set up.

First announcements will be on the mailing lists, followed by embnet.general and the bionet newsgroups

Peter will continue to work through the documentation for other applications.

4. Any Other Business

5. Next meeting

Next Monday is a holiday. Next meeting Monday 6th September, 11:00am, usual place.

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