EMBOSS: Project Meeting (Mon 5th February 2007)


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

1. Minutes of the last meeting

Minutes of the meeting of 22nd January 2007 are here.

2. Software Development

2.1 Applications

Peter plans to add a new application to report restriction digest fragments and their sequences, like digest does for proteins. This should be a simple modification to restrict with similar options.

2.2 Libraries

Alan tested the SGI compiler with full warnings. It is very good at catching cases where variables are set, set again, but never used. It also caught two references to "const const" which other compilers ignored. Alan has cleaned the warnings in all applications. Alan and Peter have cleaned the libraries.

Peter has fixed all the remaining --enable-devwarnings messages.

Peter found the ajStrRemoveWhite functions were unfortunately named the wrong way round in the last release. This has been fixed, and all current references should have been swapped. One removes excessive white space to leave single spaces, the other removes all white space. For calls looking for single words it makes no real difference, but programs should be carefully tested to make sure no behaviour has changed.

Alan has no further news on availability of purify. He will look into alternatives including other copmmercial products.

Mahmut has updated the Feta descriptions (for Taverna) with Franck Tanoh in Manchester. Applications with very little help text, for example seqret which only has sequence input and output, it is possible to automaticlaly generate text bases on the sequence type. Until now this has been hand-edited by Franck.

Mahmut has also prepared an EMBOSS distribution to be downloaded by SoapLab installers.

2.3 Other development

Peter has extended the valgring memory testing so that all QA tests now automatically generate valgrind tests. The only exceptions are those applications that need special standard input (interactive sessions with emnu and mse for example). Some tests need preprocessing, such as copying HMM files for hmmindex. These are hardcoded into the valgrind.pl script by name and will need manual editing if tests fail because of renaming.

3. Administration

Alan suggested aiming for a 4.1.0 release at the end of the month, once compiler warnings are done and new applications completed.

Alan will check with open-bio on the status of the email lists, and to get the latest download statistics from the FTP log.

4. Documentation and Training

4.1 Books

Jon has updated the text and committed the latest version to CVS. This includes information from the website on data definitions and formats, user and developer support material, tutorials and training courses.

Tim has proofread Alan's chapter on Jemboss. Alan is now updating the hardware chapter.

5. User queries and answers

The list was reviewed. Everyone should review the current list at sf.net/projects/emboss/ and close those already dealt with. Some requests have not yet been assigned to anyone.

6. AOB

7. Date Of Next Meeting

The next meeting is on Monday 19th February. We are in the other EBI meeting room again.