EMBOSS: Project Meeting (Mon 4th Jul 11)
1. Minutes of the last meeting
Minutes of the meeting of 27th June 2011 are
2. Maintenance etc.
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.
Peter fixed a reported problem drawing diamond symbols.
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.
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
Peter added a new suppression for valgrind.
3. New developments
3.1 Access methods
Alan has added server definitions for the major BioMart
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.
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.
Alan is testing on various operating systems including Irix and
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
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.
New training modules for the EBI e-Learning Portal can be developed
after the release.
6. User queries and answers
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 11th July.