= 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
1. Unzip the Opal distribution. Note that the zip file contains a root directory named `opal-server-{version}`.
1. Create an Opal home directory (to facilitate subsequent upgrades) using the command `mkdir opal-home`.
1. Create a symbolic link to the Opal server directory, using the command `ln -s opal-server-{version} opal_server`
1. Copy the `conf` directory from the server directory into the home directory, using the command `cp -r opal-server/conf opal-home`.
1. 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_databases.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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