EMBOSS: Project Meeting (Mon 8th Aug 11)

Attendees

EBI: Peter Rice, Alan Bleasby, Mahmut Uludag, Michael Schuster
Visitors:
Apologies: Jon Ison,

1. Minutes of the last meeting

Minutes of the meeting of 1st August 2011 are here.

2. Maintenance etc.

2.1 Applications

Peter has fixed a long-standing bug in indexing SwissProt with both dbxflat and dbiflat. The SwissProt description line has a "Full=" prefix which was not removed from the first word. As a result, the first word in any description was not indexed. This will be included in the first patch this week.

Peter has fixed recoder and silent to search only the forward strand. A further update is needed to correctly use the sequence range and direction.

2.2 Libraries

Michael suggested updating the template.c and template.h files. Peter will review the documentation of constants and private data definitions and make standard changes to all library source and header files.

Peter will add a refseq datatype for use in reading and managing reference sequence data. Input will use a scale value to determine whether to read all sequence data for a region or to read size data where the full sequence is not required.

Peter will also add an ACD datatype to support the AjPAssem assembly data type.

Alignment inputs are currently supported as sequence sets with the align: attribute set. We do not support our alignment formats for input, partly because local alignments do not include the full sequence. Users can report alignments in FASTA and other sequence formats that are available for input.

2.3 EDAM

Jon has committed an update to EDAM. Terms used in ACD files have been renamed. Peter has updated the ACD files and will commit them when testing is completed.

2.4 Configuration

Michael is trying to simplify the configuration script. The test for MacOSX locations for X11 libraries is now handled by autoconf. Java configuration should be able to use variables defined in autoconf. Java compilation is only used by developers as the release includes precompiled jar files. The optimization level is set to 1 for MacOSX, but could be set normally for recent releases with a test for older versions.

Autoheader has been in use for the past year. Some architecture definitions are used in ajdefine.h and some compiler definitions are used in ajarch.h. The C definitions for C++ compilers are replaced by AJ_BEGIN_DECL and AJ_END_DECL macros to avoid indentation problems in Emacs.

EMBASSY packages use their own autoheader config.h files. The plplot library has its own hand-edited config.h to define the available device drivers.

Alan is checking suggested configuration changes.

Alan proposed supporting release 2.64 of autoconf for developer builds. This is recent enough to have the major new features and should be available to all serious developers.

2.5 Other

Mahmut has made changes to pick up EDAM annotation from EBI services when writing server cache files.

3. New developments

3.1 Reference sequences

3.2 Ensembl

Michael is working on support for an ontology class used by the the Ensembl variation API.

Michael would like to to inter-convert Ensembl and EMBOSS feature tables, and to convert between coordinate systems for chromosome, supercontig and contig.

The next Ensembl release is due in September and will include some updates to variation data and support for more species.

3.3 Data access

4. Administration

Alan has released mEMBOSS 6.4.0.1

Peter has some updates that should be in a patch release. They include the SwissProt description indexing fix, a correction to use a format value from the command line for databases with more than one possible format, the patch for parsing long GFF string values, the species patch for ensemblgenomes, and the updated tcode data file.

5. Documentation and Training

5.1 Web server

Peter is still looking into a new home page. When the home page is updated we can redirect the www.emboss.org address to the new website.

Mahmut noted that the "Google search" links on the old and new websites return an error.

5.2 Books

Alan is updating the Administrator's Guide XML files to release 6.4.0.

The book XML files are now preserved in a separate CVS branch.

6. User queries and answers

All done.

7. AOB

None.

8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 15th August.