EMBOSS: Project Meeting (Mon 8th March 10)


EBI: Peter Rice, Jon Ison, Mahmut Uludag
Apologies: Alan Bleasby

1. Minutes of the last meeting

Minutes of the meeting of 1st March 2010 are here.

2. Maintenance etc.

2.1 Applications

Peter has added FASTQ files to the inputs for dbxflat in response to a user request.

Mahmut found a bug in needle where the traceback hit multiple scores. Further tests are needed to enable the code to make the correct choice by checking the gap status. The fix is committed to CVS.

2.2 Libraries

Peter is replacing system calls in library code and applications with new functions in ajsys to call exec instead of system, the unlink functions instead of 'rm', to read/write files instead of 'cp', etc. Some further testing is needed for the functions that replace system calls with redirection of standard output or standard error.

Alan will look through the new functions and add Windows versions.

2.3 Other

Mahmut is investigating Taverna timeouts. SoapLab has been updated without some unnecessary locks in the input and output specification functions. The destroy function is now unblocking and so returns faster. The reported problems are possibly related the the large size of the input files which were over 1MB.

Mahmut is looking into how to set up read timeouts, using an example user workflow and both taverna and commandline examples. When tested, Taverna had results and errors but no read timeouts. The errors were "input not defined" from nested workflows. A reply has been sent to the Taverna team and the user. It should be possible to extend the operating system timeout to help. The user will need to debug to track down the other workflow errors.

A new mEMBOSS is needed from the latest patch.

3. New developments

3.1 EDAM

Matus is visiting Jon later this week to work on EDAM and BioXSD,

4. Administration


5. Documentation and Training

5.1 Books

Jon has proofread the User book. We need to generate 4 tables.

Web site

Jon has prototyped the new web site. It is similar to the current web site but has sections with references to the books.

The HTML is generated from processing the book XML.

6. User queries and answers

All outstanding queries put on the Sourceforge tracker.

7. AOB

Peter will go to a next generation sequencing meeting in Cambridge next week.

Nobody will go to this year's Integrative Bioinformatics meeting.

8. Date Of Next Meeting

The Cambridge next generation sequencing meeting is on Monday 15th. The next EMBOSS meeting will be on Monday 22nd March.