EMBOSS: Project Meeting (Mon 1st September 08)


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

1. Minutes of the last meeting

Minutes of the meeting of 18th August 2008 are here.

2. Software Development

2.1 Applications

Alan is working on code to delete from the B+ tree indexes.

Peter asked whether this could be extended to a more detailed report on configure choices. The current .configure output could be cleaned up.

Peter has an application dbxreport to report on B+tree index contents. The profiled dbx indexing code needs to be compared to the 6.0.1 release code.

Perl applications have been contributed. They appear easy to port to C, although some help may be needed in converting code using Perl hashes.

2.2 Libraries

Fixes to the pattern library for issues with PCRE need some further testing.

2.3 SoapLab

Mahmut has EMBOSS 4 and 6 installed on the development machines. There are some issues with missing wrappers for EBI services, and the EMBOSS_DATA directory needs to be correctly set. External services still need to install EMBASSY packages for the 6.0.1 services.

A recent error was caused by a timeout limit of 5 seconds when calling showdb.

LSF tests indicated a fast turnaround time.

2.4 Jemboss

Mahmut is working on some Jemboss editor issues and some problems in printing. He noted that www.biobind.com/jemboss/ is a good source for Jemboss information.

Alan noted that Jemboss standalone installation needs the user to run install-jemboss-server.sh and say "standalone". This could be simplified to avoid confusion. Mahmut suggested using an ant script if tests can be added to the ./configure script and an error message provided to tell the user to install ant.

3. Administration

3.1 Release 6.0.0

4. Documentation and Training

4.1 Books

Jon has completed the markup of Lisa's latest updates.

5. User queries and answers

vectorsplit needs testing for effiency of processing indels.

A user reported extra blank lines in phylip matrix files.

6. AOB

7. Date Of Next Meeting

The next meeting is on Monday 15th September