EMBOSS: Project Meeting (Mon 18th January 10)
1. Minutes of the last meeting
Minutes of the meeting of 18th January 2010 are
2. Maintenance etc.
Peter is looking into recent bug reports on
the phylipnew EMBASSY package.
Alan is working on the format of the new JASPAR database.
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
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
Standard error is not reported back to
the user, for example when restrict fails
because rebaseextract has not been run to generate enzyme data
3. New developments
3.1 BioMart access
Alan is continuing to work on BioMart access code.
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.
5. Documentation and Training
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
Peter is invited to the Galaxy Developers meeting in May.
8. Date Of Next Meeting
The next meeting will be on Monday 25th January.