Generic rpms upgrade 26

From GBWiki

Introduction

This manual describes the upgrade process of Phenyx on rpms based Linux distributions from version 2.5 to 2.6.

System Setup

The current following Phenyx package must be removed prior to the upgrade:

 sudo rpm -e --nodeps perl-BatchSystem-SBS phenyx-perl phenyx-tomcat5-pwi phenyx-tomcat5 phenyx-tomcat5-demo-databank phenyx-tomcat5-docs

Phenyx Upgrade

Download Phenyx installation packages

32 bits architecture

Type the following command in a UNIX shell as root to download the Phenyx packages:

 cd /tmp
 wget -qO - "http://downloads.phenyx-ms.com/cgi-bin/getrpms.pl?version=2.6&release=stable&arch=i386"|sh
 

64 bits architecture

Type the following command in a UNIX shell as root to download the Phenyx packages:

 cd /tmp
 wget -qO - "http://downloads.phenyx-ms.com/cgi-bin/getrpms.pl?version=2.6&release=stable&arch=x86_64"|sh
 

 find /etc/phenyx -name "*.rpmsave"
 find /var/phenyx/users/ -name "*.rpmsave"

Type the following commands in a UNIX shell as root to install the Phenyx packages. (Note: replace < version > by the version number of the corresponding files in /tmp).

 rpm -Uvh phenyx-data-*.rpm phenyx-engine-*.rpm 
 rpm -Uvh phenyx-tomcat5-*.rpm

Phenyx Post Installation

Configuration of the Phenyx system

The Phenyx 2.6 post installation procedure, i.e. the configuration of the Phenyx system, is performed via a web interface. It includes the following sequential actions

• Installation of the license
• Management of the parallel setup
• Upgrade file formats for sequence databanks and users from earlier version
• Manage users

Type the following command in a UNIX shell as user phenyx (this UNIX user was created by the installer). This command is used to start the Phenyx software and the Tomcat servlet container (Web interface):

  # login from root as phenyx user (prepend 'sudo' if you're not root, but a sudoer)
  su - phenyx  
  # clean and start the phenyx server
  phenyx-service clean
  phenyx-service start

Open the following link in a web browser, log in as user phenyx (default password is phenyx, don't forget to change it in /usr/share/phenyx/tomcat5/conf/tomcat-users.xml), and follow the instructions.

 http://<your_server_name>:8080/setup/install.html

Note: As the page uses some javascript elements, please note that if you are using Realmedia player download plugin on Firefox 2, some elements might not appear. Please deactivate it and restart Firefox.

Installation and upgrade of sequence databanks

At the end of this process, you can (re-)install the databanks, following Generic_databanks_upgrade_26

Update the databank-to-Url mapping file

There is a file named databanksAc2Url.xml located in /usr/share/phenyx/ that allows to link a protein Accession code to its source file on the web (for instance the link uniprot_sprot on the protein overview). This file has to be changed, as Uniprot changed its access from www.expasy.org to www.uniprot.org.

Please therefore replace the existing file by the one here (right click and save as). Then restart phenyx (type phenyx-service stop and then phenyx-service start on a command line).

Add new quantitation methods

In order to take full advantage of the latest updates on the quantitation module, There are a few quantitation methods to add as post processing installation. The procedure to add/replace quantitation methods for Phenyx 2.6.2 is described here

Location of the tomcat temp directory

Depending on the size of your peaklist and on the disk size at /usr/share/phenyx/tomcat/temp, you might need to change the location of tomcat temp directory path with the following variable:

 export CATALINA_TMPDIR=/you/custom/path/temp

Please place this variable on the file at /etc/sysconfig/phenyx for rpms distribution or /etc/default/phenyx for debian/ubuntu distribution

Installation of Additional Third Party Software

For a number of features, such as quantitation and a few exports, Phenyx needs R statistical package to be installed. Please follow these instructions