Phenyx generic installation procedure
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System Requirements
Hardware Recommendations:
Regular Hardware requirements
- Processor 2 GHz x86 or amd64
- dual quad core (single quad core also ok), 32 GB RAM
- 1TB HDD (single partition or a /tmp with 50GB)
- Ethernet board
Optional Minimal Hardware requirements, for smaller datasets searched on SwissProt or IPI
- Processor 2 GHz x86 or amd64
- 2cores or processors, 4 GB RAM
- 300 GB HDD, one partition (NOTE: Phenyx requires approximately 10 GB, but storing results files and databanks require additional space...)
- Ethernet board
Software requirements:
- python >=2.3
- perl >= 5.8.0
- java SUN JDK >= 1.5
- make, gcc, libc6-dev
Supported OS are:
- for debian installation
- ubuntu dapper, edgy , feisty (>=5)
- debian stable (etch) , testing
- for rpm installation
- CentOS / RHEL (>=4)
- SuSe (>=10)
Other OS versions are not supported, but they should work well if the software requirements are installed.
Note: use the Linux user 'root' for installation procedure. On the other hand post-installation procedures are done with Linux user 'phenyx'
Install Phenyx on a new system
The installation procedure of Phenyx has been changed and simplified from version 2.6. The installation process of Phenyx is now divided into 2 steps:
- The first step let you check the system and installs the main components of Phenyx (core engine, the web server and the graphical interface components)
- The post installation step is a configuration setup. Tasks include the license installation, the management of the parallel setup, the configuration of users, the installation of sequence databanks.
According to your Linux distribution, follow the appropriate procedures:
- for Debian based distribution (Debian, Ubuntu)
- for rpm based distributions (RedHat, Fedora, CentOS, Suse)
Then start using Phenyx and enjoy the tool!
Upgrade to Phenyx 2.6
The upgrade procedure from version 2.5 to Phenyx 2.6 has also been simplified.
Please follow the following instructions to migrate from version 2.5 to version 2.6:
If you want to upgrade from an earlier version, please contact us
Do minor updates of Phenyx 2.6
Generic update procedure
Small patches can be made available that correct small bugs and complete a few features. To do an upgrade within version 2.6:
Open a ssh shell as user "phenyx" and type:
phenyx-service stop phenyx-service clean phenyx-service upgrade phenyx-service clean phenyx-service start
The upgrade is done. You should then be able to login and use phenyx normally.
You can also verify that the system is up and running: go to http://<your_phenyx_server_url>:8080/setup and log in with the tomcat user "phenyx" (default password is phenyx, maybe you changed it?).
You should find information about license, service should be up, parallel service should be up.
If you do have a problem, go to System check in the setup page and open the details. You can send us a copy-paste of the information there. Or even save the page as html and send it to us. And if a specific job shows an error, you can select it from the Phenyx desktop, click on the Exports link, select the "job directory archive (zip)" and send us the archive.
Specific additional installation for Phenyx 2.6.2
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). Restart phenyx (phenyx-service stop; phenyx-service start).
Add new quantitation methods
There are new quantitation methods available for iTRAQ4plex, iTRAQ8plex and TMT workflows to be installed. The procedure to add/replace quantitation methods for Phenyx 2.6.2 is described here
