EMBOSS: Project Meeting (Tue 2nd May 2006)
Jon has fixed a bug in palindrome (reporting large sequence positions) and a big in fprotdist.
Peter has completed a cleanup of all applications so that memory is freed before exit. Valgrind reports no memory still allocated for all except the database indexing programs and for a few data access methods where some minor cleanup is needed. This includes a reset function to restore the internal state of ACD processing and allow embInit to be called again. Jon and Mahmut asked whether it would be possible to create master server to invoke EMBOSS applications as function calls. Peter and Alan commented that this is possible in principle but would fail when a fatal error is encountered. One reason for the request was to cover cases where an application could rnu on one sequence or a set of sequences, to direct interfaces such as Taverna to run eiher one call for all sequences, or one instance for all sequences. Peter suggested an ACD attribute for seqall input to allow servers such as SoapLab to indicate a preference.
Peter met Andre Blavier recently and discussed future support for EMBOSSWIN. Andre is happy to help the EMBOSS team to generate a windows build. We expect some issues with system calls which were a problem in past EMBOSSWIN builds and have changed in EMBOSS since 2.10.0. We also expect some problems with limits on heap space allocation in Windows.
Support for a Windows build would allow windows clients to be cretaed, including a native Windows Jemboss client. Tim is interested in investigating this.
Peter will circulate suggestions for future partnerships and contact prospective partners with a view to further funding applications.
The release should include fixes for all bug reports on sourceforge and implementation of major feature requests. Peter noted that any features that make a significant impact on the content of the EMBOSS books (see 4.2) need to be in the release to avoid making the books out of date too soon after they first appear.
Features agreed at the meeting included:
Alan has made changes to the configuration files for the administration/installation book. Jon will work on demonstration applications for the core AJAX library function groups, and will work through the function documentation looking for any errors or omissions in the function descriptions. Together with the code cleanup (see 2.2) these are the main requirements for the programmers guide.
Jon Tim and Lisa will review the current status of the user book.
Navigation of the application pages is dificult in their current state.
Peter will generate new pages for all applications with navigation between the current CVS and last release versions. A simple apps page is still needed for other application-related pages but the /apps/ URL could be made to point to the current CVS application documentation if this can then link to the 3.0.0 release documentation and other applications pages in the headers.
Next meeting is again postponed to a Tuesday, 16th May.