|
EMBOSS: Project Meeting (Fri 19th March 2004)
|
Attendees
HGMP:
Alan Bleasby, Gary Williams, Hugh Morgan, Jon Ison, Tim Carver, Claude Beazley
Lion:
Sanger:
Cambridge Uni:
EBI:
Peter Rice, Martin Senger
Visitors:
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