|
EMBOSS: Project Meeting (Mon 7th February 11)
|
Attendees
EBI:
Peter Rice,
Alan Bleasby,
Jon Ison,
Michael Schuster
Visitors:
Apologies:
Mahmut Uludag,
1. Minutes of the last meeting
Minutes of the meeting of 31st January 2011 are
here.
2. Maintenance etc.
2.1 Applications
Alan noted that showdb is reporting the taxonomy
database twice. Peter will investigate.
2.2 Libraries
Alan corrected file open calls to require the 'b' flag, needed
on Windows.
2.3 Other
Alan has almost completed a rebuild of mEMBOSS using the latest
developer code. Some indexing issues have been identified. There is a
problem with wossname possibly related to recent changes
in embgroup.
Alan is considering extending the ajlong type to 64 bits in
mEMBOSS. This may require changes to casts between longs and ints.
The mEMBOSS build uses a list of ignored applications
in bundlewin which should be checked for any to be added or
removed.
The current documentation should be checked for the use of single and
double quotes on Unix and Windows to ensure correctness and
consistency, especially when adding the new query syntax with curly
braces.
3. New developments
3.1 EMBOSS configuration
Updated server cache files have been committed for ensembl das. The URL
for the archive was changed by a new ensembl release.
Alan will add a BioMart server cachefile.
3.2 Ensembl access
Michael will add a server cache file for ensembl.
Some Ensembl API source files have been split. This should not cause
problems for mEMBOSS.
The Ensembl API needs updating from release 58 to 61. There was a
major change in Ensembl 60 to introduce the concept of circular
sequence slices.
3.3 Query syntax
Peter has implemented a new query syntax allowing:
- lists of identifiers 'dbname:{aaa bbb ccc}'
- lists of single field queries 'dbname-field{aaa bb* ccc}'
- lists of queries across fields 'dbname-{field:aaa fieldb:bbb}'
- operators | (OR) & (AND) ! (NOT) ^ (EOR) for any of the above
The query syntax is validated against supported operators for each
access method, and is being implemented for the most used methods
(EMBOSS, EMBLCD, SRS) first.
3.4 DRCAT
Peter is adding new applications using the DRCAT database EDAM* and
Taxon annotation fields.
4. Administration
4.1 Open-Bio
Alan has created an rsync directory on the Open-Bio server.
Large binary data files will be removed from CVS and made available
through rsync. The files will be maintained by hand, updated when
database indexes and other rsync files change. When updating from CVS,
an additional rsync command will be needed.
4.2 Hardware
5. Documentation and Training
5.1 Books
Jon will finish the Developer's Guide updates tomorrow,
including updating the XML source files.
Peter will complete the User's Guide corrections later this week.
6. User queries and answers
All done.
7. AOB
None.
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 14th February.