
To run compara healthchecks
---------------------------

 cvs co ensj-healthcheck

set your environnement variable JAVA_HOME
in tcsh
 setenv JAVA_HOME /usr/opt/java141

or in bash
 JAVA_HOME=/usr/opt/java141
 export JAVA_HOME

 cd ensj-healthcheck

compile

 ./compile-healthcheck.sh

set the database.properties to point to your MYSQL server

run the healthcheck with all compara tests

 ./run-healthcheck.sh -d ensembl_compara_23_1 -output all compara_db_constraints

You can run that on just one by giving the java test case name
e.g. ForeignKeyMemberId

 ./run-healthcheck.sh -d ensembl_compara_23_1 -output all ForeignKeyMemberId

You can also run another set of healthchecks for checking the external references to
the core databases:

 ./run-healthcheck.sh -d ensembl_compara_.+ -d2 .+_core_\\d+.+ -output all \
   compara_external_foreign_keys
