Tomcat memory

View On GitHub

Many times the default memory allowance is too low. The memory requirements of WebApollo will depend on the the size of your genome and how many instances of Web Apollo you host in the same Tomcat instance, but in general, we recommend at least 1g for the heap size and 256m for the permgen size as a starting point. Suggested settings are:

export CATALINA_OPTS="-Xms512m -Xmx1g -XX:+CMSClassUnloadingEnabled -XX:+CMSPermGenSweepingEnabled -XX:+UseConcMarkSweepGC -XX:MaxPermSize=256m"

To use this setting, edit the script in $TOMCAT_BIN_DIR/ where $TOMCAT_BIN_DIR is where the directory where the Tomcat binaries reside.

Tomcat permissions

When deploying your war file to tomcat or another web application server, you may run into permissions problems in your annotations directory or your web application directory. Tomcat on many production systems will typically belong to a user and group called something like 'tomcat'. Make sure that that user can read in the tomcat "webapps" directory (where you placed your war file) and write into the annotations and any other relevant directory (e.g. tomcat/logs). As such, it is sometimes helpful to add the user you logged-in as to the same group as your tomcat user and set group write permissions for both.

No refseqs when opening up selectTrack.jsp

This problem often indicates that credentials for the LocalDbUserAuthentication script were not initialized properly because only tracks that the user has permissions for will be shown. Please refer to the quick install guide for details on these steps, paying attention particularly to the script which sets the permissions for which which refseqs a user can access.

Getting logged out when entering JBrowse

This often indicates that the script wasn't run properly, which will update JBrowse's configuration and load the Web Apollo plugin. See the data generation for details on this step.

Errors running JBrowse scripts

e.g. "Can't locate Hash/ in @INC" or "Can't locate in @INC"

If are trying to run the jbrowse binaries but get these sorts of errors, try which will initialize as many pre-requisites as possible including JBLibs and other JBrowse dependencies.

Errors during apollo deploy or

e.g. "cd: src/main/webapp/jbrowse: No such file or directory"

If you get this error, then you may need to re-run apollo deploy or even do a apollo clean-all && apollo deploy. You may also want to review the developers guide for how to create a precompiled package.

Postgres authentication setup

There are several different types of authentication methods that are used for postgres and sometimes the defaults must be customized to be used for your system.

If you get permission denied errors, make sure to review the official PostgreSQL documentation for pg_hba.conf:

The important thing to understand is that there are different types of access methods defined in the pg_hba.conf file:

  • local settings (i.e. when you are accessing the database on the command line)
  • host settings (i.e. when you are accessing the database over a socket)

With webapollo, the "host settings" are required for runtime operation, but the "local settings" are also important during setup, for example when initializing the database with the user_database_postgresql.sql.

Therefore, it is also important to understand the authentication methods:

  • peer - allows shell based logins without a password (can be used for local logins)
  • ident - based off of operating system logins (similar to shell based login but used for host/remote access. can't be used with non-operating system postgres usernames)
  • md5 - basic encrypted password based-logins (recommended for non-operating system usernames)

An ideal pg_hba.conf for WebApollo might have a line for our special local login for the web_apollo_users_admin user, as well as permitting md5 logins over host:

local   all             web_apollo_users_admin                  md5
# IPv4 local connections:
host    all             all               md5
# IPv6 local connections:
host    all             all             ::1/128                 md5

Chado export

You must install chado to use the Chado export feature, and you must also set it up for your organism. If, after setting up chado, and you receive this error:

java.lang.IllegalArgumentException: entity for parameter binding cannot be null
    at org.hibernate.impl.AbstractQueryImpl.resolveEntityName(
    at org.hibernate.impl.AbstractQueryImpl.setEntity(
    at org.bbop.apollo.web.dataadapter.chado.ChadoIO.deleteFeatures(
    at org.bbop.apollo.web.dataadapter.chado.ChadoIO.writeFeatures(
    at org.bbop.apollo.web.dataadapter.chado.ChadoJEDatabaseIO.writeFeatures(
    at org.bbop.apollo.web.dataadapter.chado.ChadoDataAdapter.execute(
    at org.bbop.apollo.web.dataadapter.chado.ChadoDataAdapter.write(

Then you must also make sure to import your genome into Chado. Refer to the configuration guide for this note on Chado export.

Differences between JBrowse and WebApollo

The "linkTemplate" track configuration parameter in JBrowse is overridden by WebApollo's feature edge matcher and drag and drop functions. It is recommended to use menuTemplate instead.