[MOBY-dev] moby grapgs updated

[Martin Senger]

As promised I am trying to find what is the problem with the Moby graphs. 
At the moment I do not know yet the solution (it is the famous situation 
that everything works fine on your laptop but stops to work when deployed 
on the publicly available server) but I will find it.

Meanwhile, you can (always) create graphs - if you need them from the
command line (assuming that you have Java installed on your computer, and
you have a 'dot' program installed).  This is a short HOWTO (which I will
put later on the jMoby pages):

1) cd <your-moby-live-dir>/Java
3) cvs update -dP
3) ./build.sh

Now you should have everything prepared on your machine. For the graphs 
try the following:

4) build/run/run-graphs-client -help
or (without reading help):

4) build/run/run-graphs-client -s -datapath GO/Object AminoAcidSequence \
                               -f result.dot
5) dot -Tpng result.dot > result.png

You will almost certainly try several times - therefore it's worth to 
cache results from the Moby Central locally. Do it by adding -cachedir 
parameter (the first time it will fill this directory, next time it will 
reuse it):

4) build/run/run-graphs-client -s -datapath GO/Object AminoAcidSequence \
                               -f result.dot -cachedir /tmp/mycache

Finally if you want to see also scufl definitions try this:

4) build/run/run-graphs-client -s -datapath GO/Object AminoAcidSequence \
                               -f result.dot -cachedir /tmp/mycache \
                               -scufl

   I will let you know when I solve the problem with my server - so you
will be able to get graphs in a more convenient way (but the way described
above should work always, disregarding our server down etc. so it is
perhaps worth to know about it I guess).

   Regards,
   Martin

-- 
Martin Senger

EMBL Outstation - Hinxton                Senger at EBI.ac.uk     
European Bioinformatics Institute        Phone: (+44) 1223 494636      
Wellcome Trust Genome Campus             (Switchboard:     494444)
Hinxton                                  Fax  : (+44) 1223 494468
Cambridge CB10 1SD
United Kingdom                           http://industry.ebi.ac.uk/~senger