EMBOSS: Project Meeting (Mon 13th July 09)


EBI: Peter Rice, Alan Bleasby, Jon Ison, Mahmut Uludag

1. Minutes of the last meeting

Minutes of the meeting of 6th July 2009 are here.

2. Maintenance etc.

2.1 Applications

Peter looked into the results of transeq when the input nucleotide sequence contains ambiguity codes. The results can be improved by better checking for unique translations of ambiguous codons. This will be added after the release.

A user requested a --version command line option. Peter has code for this which will report the EMBOSS version and any version attribute set for the applications in the ACD file (this was added only to support third-party application definitions for SoapLab 1.0). After the release this can be implemented with an extended embInitP call that also includes the EMBASSY package version number.

2.2 Libraries

Alan has fixed pen selection problems in the plplot HPGL driver and updated the pen colours.

2.3 Other

Mahmut has been testing Jemboss and fixing some minor bugs including the display of matrices used as options by prettyplot.

Peter has corrected the orientation of graphics example files, especially for density dotmatcher and pepwheel.

3. New developments

Peter has added a feature request to the tracker for strict compliance to GFF3. There are issues of multiple values, escaping of special characters (including commas), use of spaces and case sensistivity of tag names.

Jon has updated the descriptions of database entries in the dbxref.dat file. The text is taken from the database websites for resources included in responses to the ELIXIR database survey. Descriptions should include all the information needed to support searches for database discovery. The databases will be added to the EDAM EMBRACE ontology.

Peter has added a section to the Wiki for virtual databases (databases combining two or more databases, or defined as a subset of a database) and for ways to automatically discover databases by querying a server such as SRS or the ws-ebeye web service.

4. Administration

Alan has bundled the 6.1.0 release, resolving EMBASSY and mEMBOSS configuration issues and correcting compiler warnings. The SGI compiler reports additional unused variables. These need careful review before they can be removed.

X11 configuration is standardised. The method of detection of CYGWIN is improved. Checking for Xaw and Xt for the PHYLIP package has also been improved.

Testing is done on updated operating systems. The latest Debian and CentOS have been added to the list of tested operating systems.

The configuration files are updated to libtool 2.2.6.

Operating systems yet to be tested include Solaris and Open SuSe.

A few paragraphs are needed for the announcement to highlight major new features. These will include the automatic building of Jemboss and the new Wiki.

Jemboss on CYGWIN fails because it uses the gcj GNU java, but seems to work with Open JDK. Mahmut will test on the emboss machines.

5. Documentation and Training

5.1 Books

Peter will continue to work on the book texts between now and August 24th. The books will be the top priority for everyone once the release is out.

Jon has updated the list of interfaces to include MOBYLE as the successor to Pise. Peter will contact interface developers after the release to offer assistance with ACD parsing and will build an updated list of interfaces that keep up to date with EMBOSS changes.

5.2 Website

Peter will add the 6.1.0 documentation to the web site and copy the master files to the new Wiki under Appdocs.

Jon asked whether the EMBOSS tutorial could be updated. Peter suggested updating this as an EBI eLearning module.

6. User queries and answers

All done this week.

7. AOB


8. Date Of Next Meeting

The next meeting will be on Monday 20th July.