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

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

Error: Macro BackLinks(None) failed

'Environment' object has no attribute 'get_db_cnx'