EMBOSS: Project Meeting (Mon 18th January 10)


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

1. Minutes of the last meeting

Minutes of the meeting of 18th January 2010 are here.

2. Maintenance etc.

2.1 Applications

Peter is looking into recent bug reports on the phylipnew EMBASSY package.

Alan is working on the format of the new JASPAR database.

2.2 Libraries

Peter removed the BAM input code from the release as each new samtools function added required yet more additional functions. It will be rewritten from scratch before the next release.

Peter is looking into recent bug reports on refseqp sequence input.

2.3 Other

Alan noted some remaining issues with the Jemboss client/server.

wossname with 2 parameters ignores double quotes as the command line is tokenised at spaces. The tokeniser needs to be rewritten to use quotes.

Standard error is not reported back to the user, for example when restrict fails because rebaseextract has not been run to generate enzyme data files.

3. New developments

3.1 BioMart access

Alan is continuing to work on BioMart access code.

3.2 EDAM

Mahmut noted that developers in the CBS group at DTU are considering using BioXSD as a data format. This could affect the EMBOSS wrappers in the cbstools EMBASSY package.

Peter noted that the ACD relations attributes should be reviewed following the EDAM meeting in Amsterdam.

4. Administration


5. Documentation and Training

5.1 Books

Alan has reviewed the joint "Alan/Peter" to do comments.

5.1 Web site

Peter has updated the documentation pages for release 6.2.0

6. User queries and answers

None new.

7. AOB

Peter is invited to the Galaxy Developers meeting in May.

8. Date Of Next Meeting

The next meeting will be on Monday 25th January.