EMBOSS: Project Meeting (Mon 12th November 07)
Alan is still tracing a dbxflat indexing bug that only appears when EMBL release files are processed in a particular order. The crash is in removing an item from a list, but is probably caused by an error elsewhere in the code.
Peter is working through the differences between phylip 3.6 beta and the latest phylip 3.67 to bring the EMBASSY package up to date. Many of the changes to 3.61 were already included in the current PHYLIPNEW release.
Alan will check on the status of testing the MIRA fragment assembly EMBASSY code by the original author.
We have a volunteer to create an EMBASSY package for MUSCLE multiple alignment. So far he is writing the ACD file and testing all MUSCLE options work as documented. Alan's ACD wrapping approach can be used to write the remaining code.
Remaining tasks include documentation of how to write SoapLab2 ACD files and how to set up the Spinet web page front end.
Mahmut has deployed SoapLab2 at EBI. The new server has been very stable. The old server will need AppLab to be restarted soon. SoapLab2 has 142 EMBOSS tool tests and 50 tests for EMBASSY services.
Fedora 8 was released on 8th November. Alan will update the workstations.
Alan suggested drawing up a list of tasks for the release next year. One major task to consider will be updatable database indexes and a further survey of database indexing algorithms.
Jon will have complete drafts for all 3 books in the next 2 weeks. Alan and Peter will read through and update text as needed.
Jon will create templates for autogenerated text, update the contents pages, test cross references are valid, and generate everything in the format needed by the publisher.
Peter will update the current parsing scripts to generate the required text. Some new scripts will be needed to extract documentation for QA testing and other parts currently not well documented.
Jon presented an EMBOSS session to 40 EMBL predoctoral students. Many of them were unable to use a commandline interface. We need to provide clear examples of how to use programs with various interfaces to illustrate why the command line is the richest way to run the applications.
Jon has added 3 new queries to Sourceforge in the past month.
The next meeting is on Monday 26th November.