EMBOSS: Project Meeting (Mon 4th Jul 11)


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

1. Minutes of the last meeting

Minutes of the meeting of 27th June 2011 are here.

2. Maintenance etc.

2.1 Applications

Peter noted that graphics examples were rotated the wrong way after the Fedora upgrade, though it is not clear exactly when the problem first arose. Example images are fixed in the online documentation and in CVS.

2.2 Libraries

Peter fixed a reported problem drawing diamond symbols.


2.4 SoapLab

Mahmut is testing Martin Senger's latest release. The ACD grammar and parser have been updated. About 20 application tests failed. Listor and others have been updated to the 6.4.0 results. Some tests failed because group names had changed. The group names can be patched to use the previous groups.

2.5 Other

Alan is looking into cross-compilation issues after a user reported problems compiling for a 32-bit system from a 64-bit system. Any changes will be after the release. As a quick fix the target can be set to be the host.

Mahmut has fixed the Jemboss Nimbus option to restart once only when selected.

Peter added a new suppression for valgrind.

3. New developments

3.1 Access methods

Alan has added server definitions for the major BioMart sources.

Peter proposed applications that write server cache files should start with the prefix "cache".

Michael noted Ensembl 63 is released this week. The server cache files will be updated. Code updates for the previous release will be completed this week.

3.2 New applications

Peter has added new urlget application to retrieve a URL for database content retrieval from DRCAT.

3.3 EDAM

Jon reported EDAM beta 12 is released.

Two groups are interested in using EDAM for annotation.


Jon reported that DRCAT has a new home website drcat.sourceforge.net Peter has added a new resource output format of "webpage" to create the DRCAT entry static web pages.

Jon has removed the comment and contacts records in DRCAT.

4. Administration

Alan is testing on various operating systems including Irix and Solaris.

Alan has installed Fedora 15 on the EMBOSS machines. The new release has Gnome 3 and includes systemd to start daemons at boot time. 32-bit C libraries are installed, as needed by cbstools binaries.

Release notes need to include announcements of the CUP books.

Posters will be prepared this week for ISMB and the SIGs.

Alan has updated the internal wiki to MediaWiki 1.6. The wiki now shows an error and may need to be dumped and reloaded.

Alan will exclude cache directories from the backups.

Alan has defined the default group for login to the Open Bio server to be "emboss".

5. Documentation and Training

5.1 Website

Jon noted that some static pages are needed in addition to generated HTML files. These are links cited in the book texts. He will make a list.

5.2 Training

New training modules for the EBI e-Learning Portal can be developed after the release.

6. User queries and answers

All done.

7. AOB

8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 11th July.