EMBOSS: Project Meeting (Mon 23rd August 10)


EBI: Alan Bleasby, Mahmut Uludag, Michael Schuster
Apologies: Peter Rice, Jon Ison

1. Minutes of the last meeting

Minutes of the meeting of 16th August 2010 are here.

2. Maintenance etc.

2.1 Applications

2.2 Libraries

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).

2.3 SoapLab

Mahmut reported that a new version of SoapLab has been released.

2.4 Jemboss

Mahmut reports that some class names have changed in Jemboss i.e.

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.

2.5 Other

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:
   autoreconf -fi
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.

4. Administration

4.1 Patches

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.

4.2 Systems

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

5.1 Books

Alan reported that the books have now been passed by the publishers to their Production section.

6. User queries and answers

All handled.

7. AOB


8. Date Of Next Meeting

Next week is a public holiday. The next meeting will be on Monday 6th September.