EMBOSS: Project Meeting (Mon 6th July 09)


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

1. Minutes of the last meeting

Minutes of the meeting of 29th June 2009 are here.

2. Maintenance etc.

2.1 Applications

Peter has corrected a bug in testing the user-specified feature type in extractfeat where an unknown feature type would return all features. The fix currently returns only misc_features as this is the default feature type. This will be corrected to search only with a defined feature type.

2.2 Libraries

Alan has corrected the colour assignments for HP plotters in plplot. The fix uses a lookup table. We may decide to add a data file in a future release.

Peter has corrected an error in the calculation of Solexa quality scores for fastq format short read data.

2.3 Other

Mahmut has configured Jemboss to install automatically with EMBOSS.

An issue with the display of help pages is partially related to gaps in java html support, and partly issues in the generated html. Using synchronous html loading solves these problems and displays the help page correctly.

Mahmut has checked in the remaining changes in his eclipse workspace. Most of last year's Jemboss buglist are now resolved and checked in.

One remaining issue involves spaces in filenames when passed to the runtime.exe command in java. This worked on Windows but not on Unix. The fix is now working, but needs some further testing.

Alan has bundled Jemboss with EMBOSS for the release and Debian employees are currently checking a pre-release with their packaging system.

3. New developments

Peter attended BOSC 2009 to give a report on EMBOSS in the Open-Bio project updates session. At ISMB Peter presented a technology track demonstration, gave a poster presentation on the new release and future plans, and organized a 1-hour lunch time "Birds of a Feather" session on planning for the new funding period.

Peter has sent detailed reports from ISMB 20009 in Stockholm. He updated a few points from the preceding BOSC 2009 meeting, and will email the detailed BOSC report.

Peter will all public topics to the new WIKI.

4. Administration

Alan has completed tests of the candidate release on various platforms.

Alan has been looking into updating the developer configuration files to support the current libtool 2.2 version in Fedora 11.

The command "autoreconf -fi" replaces libtool 1.5 files with their libtool 2.2 versions. There is no equivalent to revert to the libtool 1.5 configuration.

Alan has been testing Fedora 11 on the EBI machines. The tests have been successful so far, but the 3 workstations to be replaced by the new ones on order will remain on Fedora 10 for now to avoid disrupting final preparation for the release.

The RAID server is now back online. There were a few warnings in the logfile which is now remotely accessible. Notify any strange problems to Alan.

Alan asked to be notified of any further issues with X11 or padding under cygwin.

Peter proposed announcing the following in the release notes:

5. Documentation and Training

5.1 Books

Peter will continue to work on the book texts between now and August 24th

5.2 Website

Peter announced the Wiki address at the Birds of a Feather session at ISMB. A few of the attendees have looked at the Wiki, but there are no new edits yet.

6. User queries and answers

All done this week.

7. AOB

Peter will attend the GMOD meeting in Oxford on August 6th and 7th. This will cover the remaining access methods on the current list for inclusion under the new grant.

8. Date Of Next Meeting

The next meeting will be on Monday 13th July, 2 days before the release.