[InterMine Dev] setting up chado (tripal) intermine

Julie Sullivan julie at flymine.org
Tue Dec 2 17:37:44 GMT 2014


Hi Sofia!

All your files look fine to me. This line from the tutorial:

	(cd ../dbmodel && ant build-db -v); ant -Dsource=chado-db -v

Assumes that your source is called chado-db. You have named your source 
in your project XML "drupal".

So try this instead:

	(cd ../dbmodel && ant build-db -v); ant -Dsource=drupal -v

Julie

----

Hello.

I am having issues trying to set up my intermine from a chado database
(actually a chado database within a tripal database).

I am following the steps in
http://intermine.readthedocs.org/en/latest/database/data-sources/library/chado/#index-0
but
feel as if I must be missing something.

ERROR:

BUILD FAILED
/data/src/intermine/imbuild/integrate.xml:54: can't find source in project
definition file: chado-db

my ~/.intermine/simrmine.properties:
db.flybase.datasource.class=org.postgresql.ds.PGPoolingDataSource
db.flybase.datasource.dataSourceName=db.flybase
db.flybase.datasource.serverName=localhost
db.flybase.datasource.port=5432
db.flybase.datasource.databaseName=drupal
db.flybase.datasource.user=xxxx
db.flybase.datasource.password=xxxx
db.flybase.datasource.maxCommections=10
db.flybase.datasource.driver=org.postgresql.Driver
db.flybase.datasource.platform=PostgreSql

my project.xml:
<source name="drupal" type="chado-db" dump="true">
   <property name="source.db.name" value="flybase"/>
   <property name="genus" value="Schmidtea"/>
   <property name="species" value="mediterranea"/>
   <property name="dataSourceName" value="Flybase"/>
   <property name="dataSetTitle" value="SmedSxl_v31 data set"/>
   <property name="converter.class"
value="org.intermine.bio.dataconversion.ChadoDBConverter"/>
   <property name="processors"
value="org.intermine.bio.dataconversion.SequenceProcessor"/>
</source>

Thanks,
Sofia



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