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EMBOSS: Project Meeting (Mon 18th January 10)
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Attendees
EBI:
Peter Rice,
Alan Bleasby,
Mahmut Uludag
Visitors:
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
None
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.