EMBOSS: Project Meeting (Mon 3rd Oct 11)


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

1. Minutes of the last meeting

The minutes of the meeting on 26th September 2011 are here.

2. Maintenance etc.

2.1 Applications

Peter has updated two command line qualifiers for prettyplot to remove dependencies on other qualifiers. They also simplify the use interface but will require wrappers to be reconfigured if they explicitly name all the options. This was needed for the Galaxy interface definitions.

Peter has updated acdgalaxy to dump Galaxy tool definitions for EMBOSS applications automatically. The definitions need testing, and will eventually include versions of the test definitions.

2.2 Libraries

Peter has moved all deprecated function definitions to the ends of the source files, and wrapped them in ifdef blocks which by default will not compile them. Two new configuration options compile the deprecated functions mentioned in the books, and all functions for sites with local code that may use them.

Mahmut reported a memory leak in ajnam.c where a server table can be created twice.

2.3 Configuration

2.4 Other

Alan has rebuilt mEMBOSS.

3. New developments

3.1 EDAM

Jon has started planning for EDAM release beta 13.


Jon has a list of possible additions to DRCAT.

Jon reported interest from MIRIAM in sharing data with DRCAT.

3.2 Ensembl

Michael has extended sequence retrieval in the Ensembl API to include fetching features with fewer memory allocations and deallocations.

3.3 Other

Alan is working on Huffman coding for compression.

4. Administration


5. Documentation and Training


6. User queries and answers

All done.

7. AOB


8. Date Of Next Meeting

The next EMBOSS meeting will be on Monday 10th October.