EMBOSS: Project Meeting (Fri 19th March 2004)


HGMP: Alan Bleasby, Gary Williams, Hugh Morgan, Jon Ison, Tim Carver, Claude Beazley
Cambridge Uni:
EBI: Peter Rice, Martin Senger

Apologies: Rodrigo Lopez Tom Oinn Thomas Laurent

Minutes of the last meeting

Minutes of the meeting of 5th March 2004 are here

1. Action points

1.1 From this meeting:

1.2 From previous meetings:

EMBOSS Ontology commit (PMR, 2003-11-28)

1.3 No longer required:

2. Software Development

2.1 AMD64, SUSE and other systems

Alan has AMD64 and SUSE Linux systems for testing.

IBM testing is delayed by problems with some compilers.

HP testing is also delayed by a lack of compilers.

2.2 Output types

Peter is adding new output types for all ACD input types, especially the phylogenetic data types. Initially these will simply return output files, but will be extended as alternative formats are implemented. The first of these to be done will probably be comparison matrices.

2.3 EMBASSY QA tests

The EMBASSY programs have been poorly served until now by QA tests. Peter is writing test cases for HMMER and other EMBASSY packages. These will take a little time to complete.

Peter has also updated QA tests to skip certain tests if required third-party packages (SRS, clustalw, primer3, etc.) are not available. The required package is added to the test definition, and a list of unavailable packages is provided on the command line when qatest.pl is run.

2.4 Domainatrix

Jon has most of the library code in nucleus, although some of Ranjeeva's code will remain in Ajax. PDB and Scop parsers will be available as function calls.

2.5 Jemboss

Tim is testing Jemboss installation. Alan reports that the editor requires Java 1.4, although SUSE Linux still only has 1.3.

2.6 MacOSX

Alan reoprts that libtool 1.5.2 now works as usual, with no changes to ltmain.sh needed.

3. Documentation & Training

3.1 Missing program documentation

Peter picks up missing program documentation in the qatest script, and will create template files for missing programs, including esim4 and meme.

4. Administration

4.1 myemboss

Peter has created a new EMBASSY package "myemboss" which will be for developers to add their own programs, or modified versions of EMBOSS programs, and to maintain cmopatibnility with future EMBOSS updates. Myemboss will contain only a few example programs (the demo* programs for example). Developers will need automake, autoconf and libtool installed to develop in myemboss, but can work with a standard (non-CVS) EMBOSS release.

Alan has modified "make install" to install the library header files for use by any programmer building their own myemboss installation.

5. User queries and answers

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

4.2 EMBOSS 2.9.0

Alan may not have the full new indexing completed in time.

Peter's graph code changes still need more work to produce a GROUT and plplot merged API.

Indexing for non-sequence data (e.g. SCOP and CATH) would be useful.

5. User queries and answers

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

6. AOB

Claude is looking into a Perl launcher for R batch submissions and the SoapLab notification system.

Peter will have a summer student working on phylip 3.6 integration into phylipnew.

7. Date Of Next Meeting

Next meeting at 9.30 on April 2nd, 2004, Shared Facilities, Hinxton