EMBOSS: Project Meeting (May 22nd 2000)


Sanger Centre: Peter Rice, Ian Longden
HGMP: Alan Bleasby, Gary Williams
Apologies: Jon Ison, Val Curwen, Tim Carver

1. Matters Arising

2. General progress on release 0.0.4

linplasmid and cirplasmid are replaced by lindna and cirdna and should be removed.

Peter has committed the changes to support PIR and BLAST format databases. PIR databases needed changes to the GCG indexing to allow for header lines with no length information. BLAST databases needed some changes to parsing the NCBI FASTA headers and code to read from the index files. NCBI BLAST 2.0 multi-file indices are not yet included.

Changes have been made to "make install" to install ACD and other files in subdirectories. The ACD processing has changed to search in the EMBOSS_ACDROOT directory, then the installation directory, and finally the original source directory. These changes will be committed later today.

Remaining code issues for the beta release are "-ossingle" not creating an output file because the output file sare generated automatically later, not creating optional output files, and linking sequences to ranges.

3. Interfaces

PISE continues to email results. This will not be updated by Pasteur for now.

Peter has written a draft "Interfaces" web page http://emboss.sourceforge.net/interfaces/ The URL will be mailed to interface developers to check on content before being made public.

4. Graphics

Ian has updated PLPLOT to release 5.0. Some checks and double buffering have been addded.So far no obvious changes have been reported, including the persistence of the X colour map bug.

A report of the bug will be posted to the PLPLOT mailing list.

5. Documentation

Gary is up to "O" in updating documentation. "octanol" needs updating by Ian and Peter.

Peter is reviewing changes to the documentation to make a standalone version that can be maintained under CVS and made into a tar distribution without the Sanger header, footer, and stylesheet processing.

The FAQ file need revision. Some of the comments are out of date.

ajCall is missing from the library documentation pages. Peter will review these.

The demo applications need to be reviewed to check their coverage of common library calls.

6. Any Other Business

7. Next meeting

Next Monday in a holiday. Next meeting on Monday 5th June, 11:00am, usual place.