EMBOSS: Project Meeting (Mon 8th March 10)
1. Minutes of the last meeting
Minutes of the meeting of 1st March 2010 are
2. Maintenance etc.
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
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
Alan will look through the new functions and add Windows versions.
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
Matus is visiting Jon later this week to work on EDAM and BioXSD,
5. Documentation and Training
Jon has proofread the User book. We need to generate 4 tables.
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.
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.