On 27 Feb 2007, at 16:23, Maximilian Haeussler wrote:
Hi,
I'm often using martshell.sh and started to like it. However it takes
quite a while to start up. I assume that this is because it is
downloading the registry from the ensembl server. The documentation
mentions "local" registry files for the clients so I've taken the file
ensembl-staging.xml from biomart-perl and trying to feed that into
martshell by exchanging defaultMartRegistry.xml with it. But the hosts
and ports in this file are not correct (127.0.0.1). Is there a better
file registry file for ensembl42's marts to download somewhere or do
you think this won't help to reduce startup time anyways?
Thanks again,
Max
Hi Max,
as the guys told you, the only 'mart way' of reducing the startup time
is to include less marts in your local registry file. Below is the file
which we use to run our central server. The file on branch 0.5 is up
to date but there is something wrong with the web cvs at sanger so
it does not show the correct file. I pasted the correct one (from
branch 0.5 biomart-perl) below. Please pick up the ones that you want:
(martj will ignore all the URLLocations)
?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE MartRegistry>
<MartRegistry>
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="ensembl_mart_42" name="ensembl" displayName="ENSEMBL 42 GENE
(SANGER)" port="3316" schema="ensembl_mart_42" user="anonymous" passwo
rd="" visible="1" default="1" martUser="" includeDatasets="" />
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="compara_mart_homology_42" name="compara_mart_homology_42"
displayName="ENSEMBL 42 HOMOLOGY (SANGER)" port="3316"
schema="compara_ma
rt_homology_42" user="anonymous" password="" visible="1" default="0"
martUser="" includeDatasets="" />
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="compara_mart_pairwise_ga_42"
name="compara_mart_pairwise_ga_42" displayName="ENSEMBL 42 PAIRWISE
ALIGNMENTS (SANGER)" port="3316" s
chema="compara_mart_pairwise_ga_42" user="anonymous" password=""
visible="1" default="0" martUser="" includeDatasets="" />
<!--
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="compara_mart_multiple_ga_42"
name="compara_mart_multiple_ga_42" displayName="ENSEMBL 42 MULTIPLE
ALIGNMENTS (SANGER)" port="3316" s
chema="compara_mart_multiple_ga_42" user="anonymous" password=""
visible="1" default="0" martUser="" includeDatasets="" />
-->
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="snp_mart_42" name="snp" displayName="ENSEMBL 42 VARIATION
(SANGER)" port="3316" schema="snp_mart_42" user="anonymous" password=""
visible="1" default="0" martUser="" includeDatasets="" />
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="sequence_mart_42" name="sequence" displayName="ENSEMBL 42
SEQUENCE (SANGER)" port="3316" schema="sequence_mart_42"
user="anonymous"
password="" visible="0" default="0" martUser="" includeDatasets="" />
<MartDBLocation databaseType="mysql" host="martdb.ensembl.org"
database="vega_mart_42" name="vega" displayName="VEGA 21 (SANGER)"
port="3316" schema="vega_mart_42" user="anonymous" password=""
visible="1
" default="0" martUser="" includeDatasets="" />
<!--
<MartDBLocation databaseType="mysql" host="aceserver.cshl.org"
database="wormmart_current" name="wormbase" displayName="WORMBASE
(CSHL)" port="3316" schema="wormmart_current" user="anonymous"
password=""
visible="1" default="0" martUser="" includeDatasets="" />
-->
<MartURLLocation default="1" displayName="WORMBASE 167 (CSHL)"
host="biomart.wormbase.org" includeDatasets="" martUser=""
name="wormbase_current" path="/biomart/martservice" port="80"
proxy="http://wwwcac
he.ebi.ac.uk:8080" serverVirtualSchema="WS_CURRENT" visible="1" />
<MartURLLocation host="www.gramene.org" name="ENSEMBL_MART_ENSEMBL"
path="/Multi/martservice" proxy="http://wwwcache.ebi.ac.uk:8080";
serverVirtualSchema="" displayName="GRAMENE (CSHL)" port="80" visible=
"1" default="1" martUser="" includeDatasets="" redirect="1" />
<MartURLLocation path="" host="www.dictybase.org" name="dicty"
proxy="http://wwwcache.ebi.ac.uk:8080"; serverVirtualSchema="dictyMart"
displayName="DICTYBASE (NORTHWESTERN)" port="80" visible="1" default="
1" martUser="" includeDatasets="" redirect="1" />
<MartDBLocation databaseType="mysql" host="martdb.ebi.ac.uk"
database="uniprot_mart_17" name="uniprot" displayName="UNIPROT
PROTOTYPE (EBI)" port="3306" schema="uniprot_mart_17" user="anonymous"
password=
"" visible="1" default="0" martUser="" includeDatasets="" />
<MartDBLocation databaseType="mysql" host="martdb.ebi.ac.uk"
database="msd_mart_4" name="msd" displayName="MSD PROTOTYPE (EBI)"
port="3306" schema="msd_mart_4" user="anonymous" password=""
visible="1" def
ault="0" martUser="" includeDatasets="" />
--
Maximilian Haeussler,
skype: maximilianhaeussler
------------------------------------------------------------------------
-------
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
------------------------------------------------------------------------
-------
