On 21 Mar 2007, at 20:35, Robert Hamon wrote:
Hi Robert,
This is a mixed biomart/ensembl problem.
I will try to answer the biomart bit then and let ensembl
web person to lend you their expertise on the rest :)
There's either a problem with the cvs for biomart or the installation
doc
for Ensembl release43 contains an error.
Trying to get biomart from cvs (yes, logged in first) using this
command:
"cvs -d :pserver:[EMAIL PROTECTED]:/cvsroot/CVSmaster co -r
release-0_5 biomart-perl"
I get this error:
"cvs server: cannot find module `biomart-perl' - ignored"
So I checked on the biomart website instead and found that using:
"cvs -d :pserver:[EMAIL PROTECTED]:/cvsroot/biomart co -r
release-0_5
biomart-perl"
works fine to get biomart from cvs.
yes, this was a recent change and it was announced on mart-dev and
ensembl-dev
mailing lists:
http://listserver.ebi.ac.uk/mailing-lists-archives/mart-dev/
msg00954.html
And to get biomart working I had to:
1- enable it in the siteconf.ini and multi.ini
2- restart the server for the perl.startup script to create
martRegistry.xml
3- run "perl bin/configure.pl -r conf/martRegistry.xml" from within the
biomart-perl folder to create/update the visible templates/datasets and
maybe some other purposes...
Now my problem is that biomart isn't integrated into the ensembl
website
like at www.ensembl.org but rather loads up filling the whole window
and
there's no theme applied, it looks really plain and confusing.
^^^
this needs ensembl web expertise
And also, after editing my marts I have to delete the
biomart-per/conf/martRegistry.xml, restart the server to rebuild the
martRegistry.xml again, and run configure.pl inside biomart-perl all
over
again... It's a very long process (1h+) and I need to do this
constantly for
the creation of our own marts. If I don't do these steps the changes
don't
show up in biomart
I used to run ensembl38 with biomart integrated very nicely and to
reload
the mart config all I had to do was delete the martRegistry.packed and
restart the server. The whole process took less then 10 minutes.
Did things really changes this much or have I not installed/been using
it
properly?
The process of configuration does not scale very well due to recent
addition of compara marts. We are now working on improving the
scalability
of this process by introducing a dataset partition, dataset extensions
and
extensible linking concepts but unfortunately this is not going to
happen immediately.
However there are some strategies which could make your life easier
right now:
1. You can create a separate registry file just for your own marts and
run configure with this only. This should be very fast so you can run
multiple times.
Once you are happy and completed your changes, you can run the long
configuration
process with the ensembl+your_mart registry only once.
2. If you are not interested in some of ensembl/compara marts you can
delete them
from the registry. As an example you can try commenting out compara
marts. This alone
should bring the configuration time down considerably.
BTW, you do not have to delete registry file. You can now have
multiple registries
and point configure.pl to to the one you want with '-r' switch. If you
want to reconfigure cleanly
you should just run it with '--clean' switch (again you do not have to
delete anything manually)
For more info look at the docs at www.biomart.org
if you need more info please drop us an email
a.
Thanks for your help.
Robert.
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Arek Kasprzyk
EMBL-European Bioinformatics Institute.
Wellcome Trust Genome Campus, Hinxton,
Cambridge CB10 1SD, UK.
Tel: +44-(0)1223-494606
Fax: +44-(0)1223-494468
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