EMBOSS: Project Meeting (Mon 23rd August 10)
1. Minutes of the last meeting
Minutes of the meeting of 16th August 2010 are
2. Maintenance etc.
Alan has modified all appropriate functions in ajstr.c/h to use
size_t and ajlong whereas previously they returned ajint values
for string lengths. This makes the library more able to use the
full memory for strings on the host machine, given that in some
instances a bit is required to specify positions from the end of
a string (negative numbers, hence ajlong is sometimes used).
Mahmut reported that a new version of SoapLab has been released.
Mahmut reports that some class names have changed in Jemboss i.e.
- org.emboss.jemboss.parser is now prg.emboss.jemboss.server
- Ajax.Util is now Util
Modifications have also been made to the Jemboss configuration
allowing the jemboss code to be rebuilt if a user defines their
own scratch space definition. This can sometimes be done via
dependencies although a 'make clean' will force a rebuild
(via an 'ant' clean).
Michael queried whether bundling of ACD files by Jemboss could be
done via ANT rather than JAR. Mahmut will investigate.
Alan, with input from Michael, has made major changes to the
EMBOSS configuration files. The system now invokes autoheader
to create configuration files (ajax/core/embossconf.h for
EMBOSS and config.h for EMBASSY). All uname usages have been
replaced with case constructs using host_os and host_cpu variables.
Automake configuration files now use AM_CPPFLAGS rather than INCLUDES.
As the autoheader system defines WORDS_BIGENDIAN, where appropriate,
the ajax source code now uses this rather than BENDIAN and LENDIAN.
All non-appropriate GNU files (e.g. 'missing', 'ltmain.sh') have
been removed from the CVS repository. All m4 files have been
tidied. Configuration now consits of just one call:
which invokes aclocal, autoconf, autoheader and automake in the
correct order. Other minor changes have been made.
Michael and Alan are considering changes to have sub-packages
such as PCRE/EXPAT use the same config header file. It is
currently deemed that configuring them as sub-packages, each
with their own configure.in, would be unworkable and probably
unnecessary. Also, it may be possible to replace the existing
large files configuration with an autoconf macro.
3. New developments
3.1 SOAP access
Mahmut has started looking at gsoap for SOAP access in EMBOSS.
Alan will look at adding gsoap configuration the the main
EMBOSS configuration procedure.
3.2 New applications
In the medium term Michael is considering an application for
dumping species information from the Ensembl servers to allow users to
see which species are available and names that can be used for their
access. Such code could potentially be used as a cacheing
mechanism. Also, in the medium term, Alan suggested that a cacheing
mechanism for registry entries could be implemented for BioMart code.
A patch file has been released containing Michael's fixes to ENSEMBL.
Ensemblgenomes can now be accessed via DB definitions. Registry
lookup has been adjusted so that applications making two sequence
calls (e.g. dottup) don't give registry warnings when used with
Ensembl. The patch file also includes a fix by Alan to prevent
rare libtool problems introduced by the first patch.
The ethernet port on Mahmut's workstation has developed a hardware
fault. As this is part of the motherboard chipset Alan will replace
it with a discrete ethernet card.
5. Documentation and Training
Alan reported that the books have now been passed by the
publishers to their Production section.
6. User queries and answers
8. Date Of Next Meeting
Next week is a public holiday.
The next meeting will be on Monday 6th September.