Installing MISO on baremetal

This installation guide is intended to be used if you cannot use Docker and Docker compose, and is not trivial to set up. We recommend using Docker compose if possible by following the Docker compose installation guide.

Prerequisites

For each service, which may be put on the same machine, the following tools are required:

Application Server:

  • JDK 11
  • Tomcat 8 or 9

Database Server:

  • MySQL 5.7.7 or MariaDB 10.2.3
  • Flyway 5.2.4 (newer versions may cause issues)

Important Note: MISO requires SSL (HTTPS) to function correctly over a network. It is usually ideal to configure SSL using a proxy server. This guide will not cover SSL configuration, but you can see an example configuration for NGINX here. SSL is not required to access MISO over a localhost connection (development purposes)

Downloading the latest release

Use the GitHub interface to download the following files for the latest release:

  • ROOT.war
  • sqlstore.jar
  • setup_files.tar.gz (for new installations only)

Setting Up the Database Server

The database server needs to have MySQL 5.7. The tool Flyway must also be present to migrate the database as the application is developed, but it can be installed on a different server so long as it can access the database server.

It is best to set a default timezone for MySQL. You can configure this in my.cnf. The simplest and recommended option is to set it to UTC by adding the following lines:

[mysqld]
default-time-zone='+00:00'

You could use a named timezone instead if you've populated the timezone tables. See the MySQL docs for more information.

The default password in the following IDENTIFIED BY clauses should be changed.

Once installed, start the MySQL console and create the database:

CREATE DATABASE lims;
USE lims;

Then add a user that has all grant access on the 'lims' db:

CREATE USER 'tgaclims'@'localhost' IDENTIFIED BY 'tgaclims';
GRANT ALL ON `lims`.* TO 'tgaclims'@'localhost';

If your database and Tomcat install are on different machines, then you will need to add a grant privilege to the MISO database from your remote machine:

GRANT ALL ON `lims`.* TO 'tgaclims'@'your.tomcat.install.server';
GRANT ALL ON `lims`.* TO 'tgaclims'@'your.tomcat.install.server' IDENTIFIED BY 'tgaclims';

Setting Up the Application Server

Download the Flyway command line tool version 5.2.4 and install it. Newer versions of Flyway may cause issues, and are not recommended.

The application server needs Tomcat 8 or 9.

Create a file called ROOT.xml in the following directory $CATALINA_HOME/conf/Catalina/localhost, creating the directory if necessary, and populate it with the following information:

<Context path="/ROOT" docBase="${catalina.home}/webapps/ROOT" reloadable="false">
  <Resources allowLinking="true"/>
  <Resource name="jdbc/MISODB" type="javax.sql.DataSource"
  driverClassName="com.mysql.jdbc.Driver"
  initialSize="32"
  maxIdle="10"
  maxActive="100"
  maxWait="1000"
  removeAbandoned="true"
  removeAbandonedTimeout="120"
  logAbandoned="true"
  testWhileIdle="true"
  testOnBorrow="true"
  testOnReturn="true"
  validationQuery="select 1"
  url="jdbc:mysql://localhost:3306/lims?autoReconnect=true&amp;zeroDateTimeBehavior=convertToNull&amp;useUnicode=true&amp;characterEncoding=UTF-8&amp;useLegacyDatetimeCode=false"
  username="tgaclims"
  password="tgaclims"/>
  <Parameter name="miso.propertiesFile" value="file:${catalina.home}/conf/Catalina/localhost/miso.properties" override="false"/>
</Context>

Make sure the database path in ROOT.xml is correct for your install:

url="jdbc:mysql://your.database.server:3306/dbname"

If you use MariaDB instead of MySQL, replace 'mysql' with 'mariadb' in the URL.

Extract the setup_files.tar.gz file and copy miso.properties to $CATALINA_HOME/conf/Catalina/localhost/miso.properties. This file contains site-specific configuration that you should review and modify as appropriate. See Site Configuration for more information.

Append the following line to $CATALINA_HOME/bin/setenv.sh or, if you installed Tomcat through apt, /etc/default/tomcat8:

JAVA_OPTS="$JAVA_OPTS -Dsecurity.method=jdbc -Xmx768M"

(Update the security method if you are using LDAP or Active Directory LDAP.)

Create the directory /storage/miso and subdirectories /storage/miso/log and /storage/miso/files. Note that these directories can be changed in miso.properties, so if you changed them, make sure to create the directories you specified instead.

mkdir -p /storage/miso/log
mkdir -p /storage/miso/files

Ensure that the user that Tomcat runs as has write permission to the storage directory. For example, if the user is in the 'tomcat' group:

chgrp -R tomcat /storage/miso/

Copy the following configuration files from setup_files.tar.gz into the /storage/miso/ directory:

File Purpose
security.properties properties to set the security environment (see below).
submission.properties properties to set the submission environment.

Security Environment (updating /storage/miso/security.properties)

MISO can use either LDAP (ldap), Active Directory LDAP (ad), or JDBC (jdbc) as an authentication mechanism. This is set by the -Dsecurity.method noted in the previous section, and the same value must be set in security.properties.

If you are using JDBC (i.e. storing usernames and passwords in the MISO database), set the security method to jdbc. No additional configuration is necessary.

For using LDAP, set the security method to ldap. Additional settings are needed for LDAP in the security.properties. Talk to your LDAP administrator.

To use Active Directory, a specific kind of LDAP, set the security method to ad. Some active directory settings are needed in addition to the LDAP settings in the security.properties file.

The search for a user is done against userPrincipalName which takes the form of an email address. To log in, the user will type their username and to do the lookup their username will be added to the domain specified in the property security.ad.emailDomain.

Use the security.ad.url property to indicate the url for the Active Directory. Some valid examples are: ad.oicr.on.ca, ldap://ad.oicr.on.ca:389 and ldaps://ad.oicr.on.ca:636.

The groups used by MISO are ROLE_INTERNAL for regular users and ROLE_ADMIN for administrators. If you find these names too general you may wish to add a prefix before adding these groups to your Active Directory. For example MISO_ROLE_INTERNAL gives a clearer indication as to what the group is used for. In this case you will need to set the property security.ldap.stripRolePrefix to the value MISO_ to allow MISO to ignore the prefix.

If using JDBC, once running, you should change the passwords of the admin and notification accounts.

Setting Up the Run Scanner

Run Scanner is a webservice that scans the paths containing sequencer output. It is not required for a functioning MISO install, but without it, sequencer runs must be added manually.

Please see the Run Scanner Installation and Setup Guide for setup instructions.

Once complete, edit $CATALINA_HOME/conf/Catalina/localhost/miso.properties of the MISO Tomcat server and set miso.runscanner.urls to the URL of the Run Scanner instance. It is possible to set up multiple run scanners managing different sequencers and add all the URLs to miso.properties. If you are adding Run Scanner to a previously-established MISO environment, restart MISO.

Installing and Upgrading

Prior to the installation, ensure that you have followed the instructions in the above and have WAR files for both MISO (ROOT.war) and, if desired, Run Scanner(runscanner-*.war).

To install or upgrade, perform the following steps:

  1. If performing an upgrade, make sure to read all release notes since the previous version you were running. Some releases indicate additional upgrade instructions, which may include
  2. Configuration changes (in miso.properties or elsewhere)
  3. Database preparation or cleanup steps
  4. Other necessary steps or warnings
  5. Backup your existing database.
  6. Stop MISO's Tomcat.
  7. Remove $CATALINA_HOME/webapps/ROOT directory and $CATALINA_HOME/webapps/ROOT.war file if they exist.
  8. Copy the new ROOT.war to $CATALINA_HOME/webapps.
  9. Migrate the database to the newest version. (Described below.)
  10. If also releasing Run Scanner, deploy it:
    1. Stop Run Scanner's Tomcat.
    2. Deploy the Run Scanner WAR.
    3. Restart Run Scanner's Tomcat.
  11. Restart MISO's Tomcat.

Migrating the database

Flyway is used to apply patches to your database to make it compatible with the new MISO version. The same path should be used for MISO_FILES_DIR as is set for miso.fileStorageDirectory in miso.properties (/storage/miso/files/ by default). SQLSTORE.JAR should be the sqlstore.jar file you downloaded.

cd ${FLYWAY}
rm -f jars/sqlstore-*.jar
cp ${SQLSTORE.JAR} jars
./flyway -user=$MISO_DB_USER -password=$MISO_DB_PASS -url=$MISO_DB_URL -outOfOrder=true -locations=classpath:db/migration,classpath:uk.ac.bbsrc.tgac.miso.db.migration migrate -placeholders.filesDir=${MISO_FILES_DIR}

$DB_URL should be in the same format as in the ROOT.xml, except replacing &amp; with just & and replacing zeroDateTimeBehavior=convertToNull with zeroDateTimeBehavior=CONVERT_TO_NULL:

jdbc:mysql://localhost:3306/lims?autoReconnect=true&zeroDateTimeBehavior=CONVERT_TO_NULL&useUnicode=true&characterEncoding=UTF-8&useLegacyDatetimeCode=false

If you run into an issue with migration V0611, ensure that the user running Flyway has read and write permissions on MISO_FILES_DIR.

If you encounter other errors migrating the database, make sure that you are using the recommended version of Flyway (see Prerequisites).