Commit 7f2b10a6 authored by Jonathan Passerat-Palmbach's avatar Jonathan Passerat-Palmbach
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Markdownify INSTALL instructions

parent 37acf293
Installation instruction (some steps may not be required on existing systems).
For Scientific Linux the Fedora steps can be followed.
Installation instruction
========================
*Some steps may not be required on existing systems.*
*For Scientific Linux the Fedora steps can be followed.*
- Log in as root
- Create two new users: useradd xnat and useradd tomcat
- Remove existing OpenJDK java packages:
- rpm -qa | grep jdk (run apt-get rpm on Ubuntu if not installed)
- `rpm -qa | grep jdk` (run `apt-get rpm` on Ubuntu if not installed)
- Remove the openjdk packages in that list. The first part is sufficient e.g. java-1.6.0-openjdk
- Ubuntu: this is not required on Ubuntu as this supports a special program that can selected the correct Java version automatically.
- Install rubygems
- Ubuntu: apt-get install ruby
- Fedora: yum install rubygems
- Ubuntu: `apt-get install ruby`
- Fedora: `yum install rubygems`
- RedHat:
- for below: replace the 7s with 6s or 5’s if that is the installed RedHat version. Replace x86_64 with i386 for systems with a 32-bit instruction set.
- yum-config-manager --enable rhel-7-server-optional-rpms (run yum install yum-utils if not installed)
- y`um-config-manager --enable rhel-7-server-optional-rpms` (run `yum install yum-utils` if not installed)
- check if rhel-7-server-optional-rpms is shown in yum repolist
- if not, probably subscription-manager should be used: subscription-manager repos --enable=rhel-7-server-optional-rpms
- yum install rubygems (confirm any required keys)
- `yum install rubygems` (confirm any required keys)
- Install puppet
- Fedora: yum install puppet
- Ubuntu: apt-get install puppet
- Fedora: `yum install puppet`
- Ubuntu: `apt-get install puppet`
- RedHat:
- for below: replace the 7s with 6s or 5’s if that is the installed RedHat version. Replace x86_64 with i386 for systems with a 32-bit instruction set.
- sudo rpm -ivh http://yum.puppetlabs.com/puppetlabs-release-el-7.noarch.rpm
- Install puppet: yum install puppet (confirm any required keys)
- Install other packages: yum install wget git mercurial (confirm any required keys)
- Update the operating system (if preferred): yum update
- Retrieve the puppet repository: git clone https://bitbucket.org/bigr_erasmusmc/puppet-xnat /etc/puppet/modules/xnat (space after puppet-xnat)
- Run install script (also runs Puppet script). sh /etc/puppet/modules/xnat/preinstall.sh
- `sudo rpm -ivh http://yum.puppetlabs.com/puppetlabs-release-el-7.noarch.rpm`
- Install puppet: `yum install puppet` (confirm any required keys)
- Install other packages: `yum install wget git mercurial` (confirm any required keys)
- Update the operating system (if preferred): `yum update`
- Retrieve the puppet repository: `git clone https://github.com/jopasserat/puppet-xnat /etc/puppet/modules/xnat` (space after puppet-xnat)
- Run install script (also runs Puppet script). `sh /etc/puppet/modules/xnat/preinstall.sh`
Notes:
------
- The output of the puppet script can be found in /puppet.out for debugging any problems (should not occur)
- The complete installation can take up to an hour depending on internet/computer speed.
......@@ -36,5 +40,8 @@ Notes:
- When XNAT is installed for the first time, an configuration window is opened when browsing to the machine web ip/address (login is admin/admin). Configure all settings. Note: you should provide the directories in which the image data should be stored. This is already configured by the puppet script, but make sure these directories have sufficient disk space available.
Known issues with installation (but rare):
- Sometimes tomcat does not shutdown properly and therefore multiple instances are running. If the website is not reachable, check with ps aux | grep java if multiple tomcat instances are running. If this is the cast, kill the processes with kill -9 [PID from ps aux] and restart tomcat with sh /usr/share/tomcat7/bin/startup.sh . After about a minute the website should be reachable.
- The installation script automatically detects the ip address of the installation machine. In some situations this does not work properly. If you cannot access the website, you can manually configure the ip-address in /usr/share/tomcat7/webapps/ROOT/WEB-INF/conf/InstanceSettings.xml on line 3. Furthermore, if it still does not work, you can set the org.restlet.autoWire param-value on false in /usr/share/tomcat7/webapps/ROOT/WEB-INF/web.xml on line 40.
------------------------------------------
- Sometimes tomcat does not shutdown properly and therefore multiple instances are running. If the website is not reachable, check with `ps aux | grep java` if multiple tomcat instances are running. If this is the cast, kill the processes with `kill -9 [PID from ps aux]` and restart tomcat with `sh /usr/share/tomcat7/bin/startup.sh` . After about a minute the website should be reachable.
- The installation script automatically detects the ip address of the installation machine. In some situations this does not work properly. If you cannot access the website, you can manually configure the ip-address in */usr/share/tomcat7/webapps/ROOT/WEB-INF/conf/InstanceSettings.xml* on line 3. Furthermore, if it still does not work, you can set the org.restlet.autoWire param-value on false in */usr/share/tomcat7/webapps/ROOT/WEB-INF/web.xml* on line 40.
......@@ -5,7 +5,7 @@ This module deploys and configures an XNAT installation using Puppet.
Installation
---------------
See the `INSTALL <INSTALL>`_ file for the prerequisites before using the puppet script. See Installation Configuration below for important settings.
See the `INSTALL <INSTALL.md>`_ file for the prerequisites before using the puppet script. See Installation Configuration below for important settings.
The puppet script installs several services and packages. The install locations vary per package. We provide the following table with the exact details per package that can be used in case of errors, later updates or partial installs/repairs. For repairing or updating a system, the puppet script can be ru-run, even the puppet script is not changed. It uses the checks that are listed in the Check column to determine if a package is already installed. If one makes the check condition false (e.g. removing the listed directory), the puppet script will re-install that specific package. Beside the checks, the puppet script will -always- copy the latest XNAT build to the tomcat webapps directory and restart the service.
......
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