EMBOSS: Project Meeting (Mon 27th July 09)
1. Minutes of the last meeting
Minutes of the meeting of 20th July 2009 are
2. Maintenance etc.
Peter has updated the FASTQ short read input and output code to
conform to standards agreed with the Bio-Python and Bio-Perl
projects. He has also fixed an issue in reading protein sequences in
"genbank" format where multiple sequence input requires the input file
to be buffered when re-reading in an alternative format. These changes
will be included in the first patch to this release. The code fixes
are being tested by Peter Cock of Bio-Python.
Mahmut has addressed 5 queries.
The run time limit for long
jobs (e.g. phylip) will be increased to 10 hours.
Mahmut will announce on the soaplab user list the SoapLab 2.2
typed interface and the update of EBI services to EMBOSS 6.1.0. Both
go live on Wednesday 29th. There are few EMBOSS interface changes,
mostly in EMBASSY packages.
Alan and Mahmut fixed issues with compilation of Jemboss
with Java 1.4.1 which is the latest version for IRIX. The last Java
release on Tru64 is 1.4.2. A Java options problem is currently under
3. New developments
Peter has added two new versions of entrails
called entrailshtml and entrailswiki to write tables of
internal data structures and definitions. We will need to also add
an entrailsbook application for the book tables, although
these are more trivial contents lists. The applications have
a -tables qualifier that selects the tables to be written, and
defaults to "all".
Alan raised an issue with releasing patches to Jemboss as
changes included a new jemboss.jar binary file which is not
covered by the current diff/patch procedures. It may be simplest to
ask users to download the jemboss.jar file separately for standalone
5. Documentation and Training
Peter has updated the sequence format sections in the books and
website. The website was very old, dating from 2002. The book also
needed updated references. Format names need to conform to the
existing names as these are being agreed with the other Open-Bio
Alan and Mahmut have updated chapters 1-4 of the Admin
Guide to cover changes to Jemboss.
Alan has started proofreading the Developers Guide. One of the
C examples needs correction. Peter will test all the C examples
as he works through the book.
Jon questioned whether some shorter sections (e.g. EMBOSS
installation introduction) could be merged into other sections.
Alan noted that some chapters could be loaded into XmlMind
while others had problems. Jon suggested this depends on
whether the DTD has been included or commented out. This can be
addressed by a simple script to (un)comment as needed to create a file
that can be reviewed.
Jon has made minor updates to some sections, e.g. removing
obsolete EMBASSY packages.
Jon raised the issue of indexing. He has a list of index terms
for all 3 books to pass to CUP. It was agreed to postpone any markup
of the original docbook files until we know what the requirements are
for the publishers. Any markup would need to be preserved in the Word
version we supply to them.
Peter will look into generating DocBook XML for the reference
guides. As there is a common source for the reference material it can
be generated as DocBook, WikiText and HTML without needing to depend
on DocBook conversions.
Peter has copied sequence format example files to the
Wiki. Some files need updating, for example EMBL, Genbank and
SwissProt to the latest format. Others are EMBOSS example output files
and should be updated to the EMBOSS 6.1.0 versions.
The same files will be added to the book CVS in the inc/text
directory. They can be included in the User Guide by default. We may
later need to edit out the less common files if they take up too much
space. They will be kept complete in the online user reference guide.
Mahmut asked whether the include files on the Wiki need to be
commented to warn against editing. Peter suggested this is not
a major problem as there is no clickable link to them and that adding
markup could be difficult as the raw text is used for generating
documentation. The application master documents could be marked up,
but adding comments in WikiText can result in additional blank lines
in the final output.
6. User queries and answers
All done this week.
Peter has mailed the Open-Bio project lists to propose common
discussions through the firstname.lastname@example.org mailing
list. All EMBOSS developers should sign up to this list and join in
the discussions which will move there from the biopython and bioperl
8. Date Of Next Meeting
The next meeting will be on Monday 3rd August.