EMBOSS: Project Meeting (Mon 23rd June 08)


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

1. Minutes of the last meeting

Minutes of the meeting of 9th June 2008 are here.

2. Software Development

2.1 Applications

Peter will test the profiled dbx indexing code on the new EMBL release 95 data.

Peter would like to add a few more new applications before the release. An example is an application to read and write a feature table.

2.2 Libraries

Peter has committed the refactored ajfile functions and corrected all deprecated function calls in the EMBOSS and EMBASSY code. This is the one remaining major source file needing cleanup for the developer's guide.

2.2 Jemboss

Mahmut has been updating Jemboss in preparation for the 6.0.0 release. Some code cleanup was needed for long functions and unused constructors. In the configuration there are changes to the locations of the working and results directories.

In the embossdata application there is a problem on Windows caused by the explicit use of the Unix "cp" command. Peter will fix this.

2.3 SoapLab

Mahmut has updated the SoapLab services to use EMBOSS 5.0.0 (from 2.8.0 that was used for myGrid). The legacy "derived services" are retained for now. The services need to be switched to use LSF before migrating to the new servers.

SoapLab2 uses a circular logging system which loses old records. Monitoring shows 250 jobs per day using the new SoapLab2 services, and a similar figure for the SoapLab1 services.

3. Administration

3.1 Funding

Peter and Alan are looking into funding sources for 2009.

4. Documentation and Training

4.1 Books

Jon has updated the Administrator's manual and commited the changes. Peter will contribute a section on installing the MYEMBOSS EMBASSY package.

4.2 Website

Jon has updated the application descriptions. Peter will copy these into the ACD files so that they are automatically updated everywhere.

Some applications are noted in the SourceForge trackers as needing further attention from experts in their algorithms.

5. User queries and answers

No new issues.

6. AOB

Alan has installed Fedora 9 on the developer machines.

7. Date Of Next Meeting

The next meeting is on Monday 7th July, the last meeting before the release.