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Subject: remove extension to call libdbix-dbstag-perl binaries
Description: libdbix-dbstag-perl binaries have perl extension removed,
current scripts must call those binaries without extension too
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 19/03/2012
--- a/INSTALL.Chado
+++ b/INSTALL.Chado
@@ -367,17 +367,17 @@
the Sequence Ontology (SO) is absolutely required for proper
functioning of the database. The commands to load an ontology are:
- $ go2fmt.pl -p obo_text -w xml /path/to/obofile | \
+ $ go2fmt -p obo_text -w xml /path/to/obofile | \
go-apply-xslt oboxml_to_chadoxml - > obo_text.xml
This creates a chadoxml file of the obo file - then execute:
- $ stag-storenode.pl \
+ $ stag-storenode \
-d 'dbi:Pg:dbname=$CHADO_DB_NAME;host=$CHADO_DB_HOST;port=$CHADO_DB_PORT' \
--user $CHADO_DB_USERNAME --password $CHADO_DB_PASSWORD obo_text.xml
If you have other ontology format files, the commands are similar;
-consult the documentation for go2fmt.pl and go-apply-xslt for your
+consult the documentation for go2fmt and go-apply-xslt for your
file format.
It is a good idea at this point to make a back up of the database,
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