EMBOSS: Project Meeting (Aug 2nd 2000)

Attendees

HGMP: Val Curwen, Alan Bleasby, Jon Ison, Tim Carver
EBI:
Apologies: Gary Williams

1. Matters Arising

Alan reported theat All EMBOSS data file names have been changed so that they begin with an 'E' although the names of databases remain unchanged. Gary has changed the documentation and web pages accordingly.

The Sanger web pages have been redirected to the HGMP.

2. Developments

A bug has been fixed in the transeq program, which was producing short translations in some cases. Other programs using ranges and seqall should be checked

EMBOSS will work in most instances with 64 bit compilation if (under Solaris) instances of ftell / fseek are replaced with ftello / fseeko or (for SG's) ftell64 / fseek64. There are only a few places where "long long" definitions need adding. Therefore EMBOSS is capable of working with files of 2GB and greater. Appropriate preprocessor directives will be added to the source as needed.

Johann Visagie has ported EMBOSS to FreeBSD, which will appear in the 'ports' directory of appropriate ftp / web servers. Johann had mentioned that a list of any new files that had been submitted would be useful. This could be generated automatically with a shell script.

EMBOSS is no longer dependent on the $HOME environment variable.

ajnam.c has been fixed for the showdb program, which was not reporting GCG indexes properly.

A documentation directory hierarchy has been created.

Alan and Val reported: There is a problem with -sbegin; if the value for sbegin exceeds the length of the sequence, a single residue/base is returned in the output, which is not appropriate behaviour.

There is a configuration problem using EMBOSS with PURIFY at the HGMP. We have found a temporary workaround but needs a firmer fix as it will probably be a problem elsewhere.

People using EMBOSS with eXceed should configure it to have Screen Definition->Server Visual set to pseudocolour. This removes the error messages seen by Tim and Val when using EMBOSS in teaching at some sites, and also reported to the EMBOSS mailing list.

Val suggested that anyone outside the group who makes a major contribution to EMBOSS gets a free T-shirt - what more incentive do people need? :)

Val has completed an article on EMBOSS for EMBNet News.

David Martin is writing a systems administration guide to EMBOSS.

3. Date Of Next Meeting

Next meeting to be held on Monday 7th August, HGMP