EMBOSS: Project Meeting (Mon 9th May 11)
1. Minutes of the last meeting
The last 3 meetings were cancelled (vacations and two public
holidays). Minutes of the meeting of 11th April 2011 are
2. Maintenance etc.
Peter fixed a bug in dbifasta which failed when an ID
line failed to parse, and another bug which prevented the
specification of one of the GCG format variants.
New applications documentation has been uploaded to the EMBOSS Wiki.
Mahmut will look into a fix for HTTP redirects where the host
address is missing.
Peter suggested extending the version number to 188.8.131.52 so that
EMBOSS will have the same length version number on Unix and
Windows. This will greatly simplify the tests for output content in
Mahmut asked whether EMBOSS should support multiple sequence
regions in GFF files. Peter will investigate, but it is likely
that this would complicate the inclusion of sequence data so the
current interpretation of one sequence region per GFF file (until the
next GFF header) will remain.
Peter will modify the handling of unknown feature tags sin GFF
so they will appear under their original name. They can be
automatically converted to 'note="*tag: value" form on input, and
converted back on output.
Peter has modified the qatest.pl script to work on
Windows with the Visual Studio 2010 build. The script now auto-detects
Windows using the output of embossversion which now reports
"windows" as the system. There are minor issues with the locations of the
emboss.standard and emboss.default files and the server cache files
which Alan will be consulted on.
The modified script can now automatically find the test and
documentation directories and so can be run from anywhere, always
storing the results in the test/qa subdirectories.
File names are reported as a mixture of POSIX and Windows where EMBOSS
reports the filename string. A function is needed to generate a clean
Windows name for Windows installations.
Mahmut has completed the move of SoapLab to the London servers.
These can now be upgraded to EMBOSS 6.3.1. External Services have
requested changes for message path names in WSDL to be parameters, but
this would break BioCatalogue and EMBRACE registry scripts.
Mahmut has added a method (GetSomeResults) to return partial
SoapLab job results. XML typing issues were resolved.
HTTP links to the Spinet interface were fixed.
Mahmut is working on Jemboss input types. Feature inputs are
not working, and output formats need to be added for the new data
3. New developments
3.1 Access methods
Mahmut has successfully retrieved sequences and features from
a CHADO server. The code has been checked in.
One DAS access test is currently failing. Mahmut will try to
improve DAS feature mapping.
3.2 Query language
Peter fixed a bug in query language processing where two
regular expressions are tested, but strings are extracted from the second
expression only for validation. More QA tests are needed to rigorously
check parsing, especially for bad query strings.
Jon is writing up EDAM, and completing the latest cleanup.
3.4 New applications
New applications for the release were discussed. Peter plans to
add applications to use cross-references from UniProt and
EMBL/GenBank, Go, and the NCBI taxonomy to refine results and searches.
We should also add applications that populate and report on assembly
input objects from BAM or SAM format files.
Peter has a 10 minute talk on EMBOSS new developments at BOSC and has
submitted an ISMB technology track demonstration.
Jon has submitted an EDAM presentation to the Bio-Ontologies SIG.
Peter has ordered a replacement backup drive for emboss5.
5. Documentation and Training
6. User queries and answers
8. Date Of Next Meeting
The next EMBOSS meeting will be on Monday 16th May.