EMBOSS: Project Meeting (Mon 6th Mar 2006)


EBI: Peter Rice, Jon Ison, Alan Bleasby, Rodrigo Lopez
Sanger: Tim Carver
Apologies: Lisa Mullan

1. Minutes of the last meeting

Minutes of the meeting of 20th February 2006 are here

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 http://www.fsf.org/licensing/licenses/index_html#GPLCompatibleLicenses 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 text.

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 share/EMBOSS/doc/html/embassy/package and share/EMBOSS/doc/programs/text

These changes are a necessary first step to making separate documentation trees for each release and for the current CVS code on emboss.sf.net.

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. Administration

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 documentation.

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.

6. AOB

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.