EMBOSS: Project Meeting (Mon 6th Mar 2006)
1. Minutes of the last meeting
Minutes of the meeting of 20th February 2006 are
2. Software Development
2.1 XML DOM parsing
Alan is investigating the domc library which has
the MIT licence. Peter confirmed that this is compatible with
the LGPL licensing of the EMBOSS libraries. See
for details of compatible licences. Integrating the domc library will
involve changes to hashing functions.
2.2 Auto generated documentation
Peter has updated autodoc.pl, the script that generates the
documentation. We have been maintaining the program documentation
master copies on the emboss.sf.net website, and building HTML and
text files from the sourceforge web pages to generate the release
documentation in doc/programs/html and doc/programs/text. The master
documentation is now maintained in doc/programs/master/emboss with the
same template files as currently on sourceforge.
The master templates are used to generate the HTML and text files
through a simple Perl parser to resolve include files. This replaces
the previous use of lynx to copy HTML from the sourceforge
website. Lynx is still used to convert the generated HTML files to
Make install will install the documentation in
share/EMBOSS/doc/html/emboss/apps (for locaL HTML
Documentation) and share/EMBOSS/doc/programs/text (for TFM).
This change allows EMBASSY documentation to be cleaned up. The EMBOSS
main package no longer has the EMBASSY documentation under
doc/programs. It is moved to emboss_doc/master emboss_doc/html and
emboss_doc/text under each EMBASSY package, and installs into
These changes are a necessary first step to making separate
documentation trees for each release and for the current CVS code on
2.3 HMMER update
Jon is QA testing the resolution of ambiguity codes for HMMER -
an issue resolved in HMMER 2.3.2
2.4 QA testing
Peter has updated all QA test results to treat the Linux results
on the emboss machines as standard. A few PHYLIP programs gave
slightly different results on Linux and Tru64.
2.5 sixpack update
Rodrigo has an update to sixpack to emboss-submit
which adds extra transeq functionality.
3.1 Marc Colet visit
Marc Colet from the Belgian EMBnet node visited to discuss the
wEMBOSS interface and the future of EMBOSS. The discussion included
ACD changes, integration of blast, data files, and many other
topics. Jon and Marc will write up a summary.
4. Documentation & Training
4.1 CVS browser
Rodrigo recommended the "fisheye" browser for the CVS
repository, although this requires a server on sourceforge (EMBOSS
code is on open-bio.org).
Peter noted that SourceForge is now offering subversion as a
CVS server. Probably best to wait and see how sourceforge
develops. Currently performance can be rather slow and open-bio.org
has been an excellent CVS server so there are no plans to change.
4.2 Application documentation
Jon has written a descripion of how to produce new application
4.3 Website updates
Peter will put the new meeting schedules on the website (and
add the missing minutes).
5. User queries and answers
Jon reported on outstanding user queries from the past 2
weeks. All have been resolved.
Jon is learning Taverna
architecture, using Ranjeeva's pipelines as test cases. Some of the
control logic may require features expected in Taverna 2.0
7. Date Of Next Meeting
Peter and Alan will be away on March 20th (EMBRACE project AGM). Peter
will be on vacation on April 7th. Monday April 17th is a holiday in
the UK and is followed by the developers course (18th-20th).
So the next scheduled meeting is in 2 months time.
Next meeting at 9.30 on Tuesday 2nd May 2006.