EMBOSS: Project Meeting (Mon 6th July 09)
1. Minutes of the last meeting
Minutes of the meeting of 29th June 2009 are
2. Maintenance etc.
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.
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.
Mahmut has configured Jemboss to install automatically with
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
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
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.
Alan has completed tests of the candidate release on various
Alan has been looking into updating the developer
configuration files to support the current libtool 2.2 version in
The command "autoreconf -fi" replaces libtool 1.5 files with their
libtool 2.2 versions. There is no equivalent to revert to the libtool
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
Alan asked to be notified of any further issues with X11 or
padding under cygwin.
Peter proposed announcing the following in the release notes:
- The new EMBOSS Wiki
- Making documentation files available on the Wiki for community editing
- Possible increased frequency of releases under the new funding
- Offers to maintain ACD parsing for any group needing help in
keeping up with changes to ACD and applications for each new release
5. Documentation and Training
Peter will continue to work on the book texts between now and
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.
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.