EMBOSS: Project Meeting (Mon 24th November 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 10th November 2008 are here.

2. Software Development

2.1 Applications

Alan is working on the ememe and emast EMBASSY wrappers to version 4.0 of the meme package. The new release has new output options to write a single text file, or to write four files to a named directory. A good solution would be to split meme into two applications, one for each output option. For the multiple files output a temporary directory will be used in the wrapper, with the results moved to the current directory on completion. The temporary directory will not use /tmp to avoid complications in the Windows code.

emast currently has problems with references to a local file in the ememe output, described as "DATAFILE=" but missing after ememe has run. This is the temporary file used to rewrite the user input as FASTA format. Peter will check how the QA tests manage to work around this.

Peter has a bug in the profiled dbx indexing code. This may be related to an error in saving the description index on an earlier run.

2.2 Libraries

Peter has committed all recent changes to CVS. These include sequence input format updates for PDB and GenBank-related formats, and corrected SwissProt output.

2.3 SoapLab

Mahmut has revised the previous work on typed services and DAS GFF outputs. A web application was deployed to Tomcat for testing.

A user reported problems using a Taverna client. This appeared to be a client side problem. A new report indicates that there are server issues which are now resolved. The problems are where Taverna sends a workflow with multiple SoapLab requests to Tomcat for remote execution.

Modifications were made to synchronize usage of AXIS objects, using the alltools library in Java.

Rare JAXWS client side errors were fixed by updating to the most recent JAXWS version. This release has changed parsers but this does not seem to cause any problems.

Users have requested a single Taverna plugin. Mahmut has inquired about developer access to Taverna to merge the SoapLab plugins.

Mahmut is invited to a Taverna workshop in February.

A bug in the shell script used for cleaning cron jobs can lead to a "directory not found" error when running find on large directories. The script is now changed to use the "-mindepth" option which avoids deleting the top level sandbox directory.

Mahmut has compared SoapLab metadata with the Galaxy project. Galaxy's metadata is 5-10 times shorter and has an explicit commandline description with parameter variables. For large numbers of parameters, Galaxy supports multiple HTML forms with page tags for "input", "output", etc. Test descriptions are included in the metadata.

EMBRACE partners in Bari and MPI have received help in testing services. Two SoapLab services have been added to the EMBRACE registry as placeholders. The full set will be submitted when the registry API is released.

2.4 Other

Peter made a minor change to the java.m4 file to remove extra space from the "./configure --help" output. This may need to be copied to the EMBASSY directories

3. Administration

Alan has asked OpenBio for an update on the proposal to move the EMBOSS website.

Peter noted that Sourceforge have restored interactive access so that website updates can again be made through CVS.

Alan will download the Fedora 10 release and test before installing on the EMBOSS machines.

Alan notes that a new "autofs" release may fix the automount problems.

Mahmut noted that the new Netbeans release can import an eclipse project.

4. Documentation and Training

Postponed to the next meeting.

5. User queries and answers

Alan will look into recode

6. AOB

From January 2009 meetings will start 30 minutes later (10:00) to avoid the fire alarm test. The meetings are booked in the Hall View Room in the EBI East Wing.

7. Date Of Next Meeting

The next meeting is on Monday 8th December.