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EMBOSS: Project Meeting (Mon 3rd Oct 11)
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Attendees
EBI:
Peter Rice,
Alan Bleasby,
Jon Ison,
Michael Schuster
Visitors:
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.
3.2 DRCAT
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
None.
5. Documentation and Training
None.
6. User queries and answers
All done.
7. AOB
None.
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 10th October.