
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_.+ -d .+_core_\\d+.+ -output all \
   compara_external_foreign_keys


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

Use new healthcheck system to access databases in possibly two separate MySQL instances to check compara against corresponding core DBs
Use new healthcheck system to access databases in possibly two separate MySQL instances to check compara against corresponding core DBs
