[EMBOSS] Bootstrap

[Mahmut Uludag]

Hi Achille,

> /homes/tc_user/.lsbatch/1241512944.708672: line 8: 14611 Segmentation fault
>  (core dumped) /ebi/extserv/bin/EMBOSS-4.1.0/bin/fneighbor -datafile

It looks like fneighbor program is not happy with the input data
provided. Unfortunately a bug in EMBOSS version 4.1 doesn't let error
messages printed but the program crashes. However if I run the same
input data with latest EMBOSS (6.0.1) I get the following error
messages.

        Error: Distance file i_datafile: Row '  3.527346' has 9 values
        Error: Distance file i_datafile: Row '  5.470720' has 8 values
        Error: Distance file i_datafile: Row '  4.804096' has 8 values
        ............
        Error: Distance file i_datafile: Row 'ACC97187.1' has 11 values
        in square format
        Error: Distance file i_datafile: Row '  0.000000' has 8 values
        Error: Distance file i_datafile: Row 'NP_082292.' has 0 values
        in square format
        Error: Distance file i_datafile: Row '  4.733737' has 8 values
        in square format
        ............
        Error: Distance file i_datafile: Row '  4.151302' has 8 values
        Error: Distances file found 2 rows, expected 15
        Error: Unable to read distances file 'i_datafile'

It would be advisable to use EBI main Soaplab services which includes
EMBOSS-6.0.1 applications, instead of Soaplab services for EMBOSS 4.1
which is selected by default in Taverna-1.7.1. You can make this change
by editing taverna.defaultsoaplab entry in your taverna
conf/mygrid.properties file as follows.

  taverna.defaultsoaplab = http://www.ebi.ac.uk/soaplab/services

After this change you need to restart taverna and delete and redefine
your Soaplab Processors (if it is too much work then you can at least
redefine fneighboor Processor as it is crashing with EMBOSS-4.1 and use
main Soaplab services for Processors you will define in future).

I cc this message to Alan and Stuart from Taverna team for information.
They were planning to change default Soaplab endpoint to main EBI
Soaplab services in the next release of Taverna-1.7 series.

Regards,
Mahmut