EMBOSS: Project Meeting (Mon 7th February 11)


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

1. Minutes of the last meeting

Minutes of the meeting of 31st January 2011 are here.

2. Maintenance etc.

2.1 Applications

Alan noted that showdb is reporting the taxonomy database twice. Peter will investigate.

2.2 Libraries

Alan corrected file open calls to require the 'b' flag, needed on Windows.

2.3 Other

Alan has almost completed a rebuild of mEMBOSS using the latest developer code. Some indexing issues have been identified. There is a problem with wossname possibly related to recent changes in embgroup.

Alan is considering extending the ajlong type to 64 bits in mEMBOSS. This may require changes to casts between longs and ints.

The mEMBOSS build uses a list of ignored applications in bundlewin which should be checked for any to be added or removed.

The current documentation should be checked for the use of single and double quotes on Unix and Windows to ensure correctness and consistency, especially when adding the new query syntax with curly braces.

3. New developments

3.1 EMBOSS configuration

Updated server cache files have been committed for ensembl das. The URL for the archive was changed by a new ensembl release.

Alan will add a BioMart server cachefile.

3.2 Ensembl access

Michael will add a server cache file for ensembl.

Some Ensembl API source files have been split. This should not cause problems for mEMBOSS.

The Ensembl API needs updating from release 58 to 61. There was a major change in Ensembl 60 to introduce the concept of circular sequence slices.

3.3 Query syntax

Peter has implemented a new query syntax allowing: The query syntax is validated against supported operators for each access method, and is being implemented for the most used methods (EMBOSS, EMBLCD, SRS) first.


Peter is adding new applications using the DRCAT database EDAM* and Taxon annotation fields.

4. Administration

4.1 Open-Bio

Alan has created an rsync directory on the Open-Bio server.

Large binary data files will be removed from CVS and made available through rsync. The files will be maintained by hand, updated when database indexes and other rsync files change. When updating from CVS, an additional rsync command will be needed.

4.2 Hardware

5. Documentation and Training

5.1 Books

Jon will finish the Developer's Guide updates tomorrow, including updating the XML source files.

Peter will complete the User's Guide corrections later this week.

6. User queries and answers

All done.

7. AOB


8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 14th February.