EMBOSS: Project Meeting (Mon 1st October 07)


EBI: Peter Rice, Alan Bleasby, Martin Senger, Mahmut Uludag
Apologies: Jon Ison, Shaun McGlinchey, Rodrigo Lopez, Tim Carver

1. Minutes of the last meeting

Minutes of the meeting of 17th September 2007 are here.

2. Software Development

2.1 Applications

Alan has made modifications to the Windows builds for the 3 new applications added since the release.

Alan is testing a dbxflat indexing bug that only appears when EMBL release files are processed in a particular order.

Peter reported that Jingchu has asked about coderet supporting features that join across more than one entry.

2.2 Libraries

Peter has a modified acdpretty that preserves comments in ACD files. It needs a few more changes to support inline comments better, especially in quoted attribute values.

2.3 SoapLab

Mahmut has tuned garbage collection on the SoapLab server to be allowed to use more time and has updated the Axis version. The server is now much more stable and processed 3000 jobs in the past week. The XML library will be updated to the latest version.

Mahmut has web services using a JAX-SW API and the dispatch server API with proper typing. These can use Java introspection to give a generic way to run jobs and can potentially be automated for all EMBOSS applications without any additional Java code.

Martin has committed the JAX-WS web services layer for SoapLab2, with documentation to be updated in the next few days. Some work is needed for features of EMBOSS applications - the old SoapLab had a perl utility script to collect all outputs in a given directory which needs to be replaced with java code using the current ACD parser. Work will continue on this and the new ACD parser (with Shaun in the next 2 months. The "ACD dashboard" is still planned as a future project.

2.4 Other development

3. Administration


The fix Alan provided for primer3 launching did not work for the user who reported the original problem, but the user suggests it may be an installation issue.

4. Documentation and Training

4.1 Books

4.2 Website

The FAQ page (and the FAQ file in the distribution) were updated by Jon to describe the new libgd version that supports GIF graphics format.

5. User queries and answers

Peter noted that multiple sequences in GFF2 format (without features) appear to be broken.

6. AOB

7. Date Of Next Meeting

The next meeting is on Monday 15th October.