Opal HowTo Install ¶

Tags: HowTo Opal

See: ​http://wiki.obiba.org/display/OPALDOC/Opal+Installation+Guide

Process ¶

We followed the Installation of Opal Zip distribution instructions that installed Opal from a zip file.

1. Download Opal distribution into the /local/ directory
2. Unzip the Opal distribution. Note that the zip file contains a root directory named opal-server-{version}.
3. Create an Opal home directory (to facilitate subsequent upgrades) using the command mkdir opal-home.
4. Create a symbolic link to the Opal server directory, using the command ln -s opal-server-{version} opal_server
5. Copy the conf directory from the server directory into the home directory, using the command cp -r opal-server/conf opal-home.
6. Create a script called start_opal.sh in the /local/ directory containing the following:

#!/usr/bin/env bash

echo "Starting Opal"

export JAVA_OPTS="-Xmx2G -XX:-UseCompressedClassPointers"
export OPAL_HOME="/local/opal-home"

/local/opal-server/bin/opal

echo "Ended"

The java options are:

-Xmx2G

increase the memory allocated to Java to 2GB

-XX:-UseCompressedClassPointers

Do not compress class pointers (because Opal creates too many classes?)

Running as wwwrun ¶

Permissions ¶

The following permission changes should be used to make Opal run as wwwrun, but they don't work yet!

find /local/opal-server -type d -exec setfacl -m d:u:wwwrun:rwx {} \;
find /local/opal-home -type d -exec setfacl -m d:u:wwwrun:rwx {} \;
find /local/opal-server -type d -exec setfacl -m u:wwwrun:rwx {} \;
find /local/opal-home -type d -exec setfacl -m u:wwwrun:rwx {} \;

Starting Opal ¶

So this doesn't work either.

sudo -u wwwrun /local/start_opal.sh

Olly says in his documentation that you shoudl be able to start Opal bin running opal-server/bin/opal start. I need to check this oout when it's running properly.

ToDo: This needs to start on boot

Opal Post Installation ¶

See:

• ​http://wiki.obiba.org/display/OPALDOC/Post+Installation+Set-up

Opal Database Setup ¶

See:

• ​http://wiki.obiba.org/display/OPALDOC/Databases+Administration

1. Update MySql Config ¶

1. The config file for MySQL files on a LAMP server is stored at /db/mysql/etc/my.cnf
2. Change the default character set in the [mysqld] section:

default-character-set=utf8
default-collation=utf8_bin

3. Change the storage engine in the [mysqld] section:

default-storage-engine=INNODB

Actually these both look OK, with the exception that the collation is utf8_general_ci, so I will just change that

2. Create Databases ¶

1. Create the following script:

# Create Opal database and user.
#
# Command: mysql -u lampuser -p < create_opal_database.sql
#
 
CREATE DATABASE opal_data CHARACTER SET utf8 COLLATE utf8_bin;
 
CREATE USER 'opal_data' IDENTIFIED BY '<opal-data-user-password>';
GRANT ALL ON opal_data.* TO 'opal_data'@'localhost' IDENTIFIED BY '<opal-data-user-password>';
FLUSH PRIVILEGES;

CREATE DATABASE opal_identifiers CHARACTER SET utf8 COLLATE utf8_bin;
 
CREATE USER 'opal_identifiers' IDENTIFIED BY '<opal-identifiers-user-password>';
GRANT ALL ON opal_identifiers.* TO 'opal_identifiers'@'localhost' IDENTIFIED BY '<opal-identifiers-user-password>';
FLUSH PRIVILEGES;

2. Change the passwords to something appropriate
3. Run the script like it says in the command comment at the top of the script.

Installing RServe ¶

Resources ¶

• ​https://rforge.net/Rserve/
• ​https://rforge.net/Rserve/doc.html
• ​http://cran.r-project.org/web/packages/Rserve/Rserve.pdf

Installation ¶

Again from Olly's notes:

sudo -u wwwrun R
install.packages('Rserve')

• When you install the package in R it puts a folder called R in your home directory. Several Layers down this you will find the RServe binary. Mine in at ~/R/x86_64-suse-linux-gnu-library/3.1/Rserve/libs/Rserve. At the minute it errors that it doesn't know where the R home directory is, but hopefully I can find that out from somewhere.

ToDo: This needs to be started on reboot. An example of how to do it can be found at: ​http://wiki.obiba.org/display/OPALDOC/R+Server+Installation+Guide.

Installing DataShield ¶

See:

• ​http://datashield.org/documentation/administrators.html#serversetup
• ​http://wiki.obiba.org/display/OPALDOC/Opal+DataSHIELD+User+Guide

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