Generic databanks installation 26
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Introduction
Phenyx has developed a graphical interface to install and maintain sequence databanks. This feature is available for all users having the privileges to do so. The databanks to be made available for all users have to be installed by the phenyx user "default". The databanks installed by another user are available for this user only.
To allow / prohibit a user to install and maintain databanks, edit the file /var/phenyx/users/<the_user_name>/user.properties and attribute a true or false property to the user.databanks.hasprivate= line.
Installation of Sequence Databanks during an Installation of Phenyx 2.6 from Scratch
In the Phenyx installation procedure, a number of default databanks are already prepared to be installed and used by all users. These are SmallTestDB (a collection of about 20 proteins dedicated to test Phenyx), uniprot_sprot and uniprot_sprot_decoy. In addition, the taxonomy is also ready to be installed.
- To initialise Phenyx with the prepared databanks, follow the process as described in Install Prepared Databanks
- To install new databanks, follow the Databank Manager documentation.
Installation of Sequence Databanks during an Upgrade to Phenyx 2.6
During the upgrade procedure, the databanks files have been modified. As the format is slightly changing from 2.5 to 2.6, the procedure has removed most of the index, config and binary files for all databanks, except for the Phenyx-fasta formatted file and the version information. You therefore need to prepare the databanks from this file.
- To initialise Phenyx with the prepared databanks and the databanks installed in the previous version and made accessible to all users, follow the process as described in Install Prepared Databanks
- Upgrade the databanks attributed to specific users (private databanks) by following the Specific usecase Upgrade_Private_Databanks
Install Prepared Databanks
Login to Phenyx with the user default
Note:You previously should have set the password for this user named 'default' in the page
http://<your_server_name>:8080/setup/install.html
at point 4) Manage Users, section 2. Default user: You need to set a password for the user default.
http://<yourserver>:8080/pwi
From the Desktop, click on the Management Console link
Select the DB manager link in the Management Console
For each databank select the link + new version
In the pop-up window, the default installer is upgrade. Click on the submit button.
To refresh the status of the databanks version, click on the 
icon on the Databanks list viewer.
Note 1: In case the databanks do not appear:
- Click on the arrow on the top-right of the database hierarchy window to hard-refresh the list.
- If you use Firefox 2, make sure to deactivate plugin that can be in conflict with javascripts, such as the Realmedia Player download plugin.
Note 2: The default installer creates a SmallTestDb database and a uniprot_sprot_decoy as well. SmallTesDb is a collection of about 20 protein entries to start and test Phenyx with the test datasets provided in the example 1 of the training exercises page and a few others. uniprot_sprot_decoy is an example of a decoy database related to uniprot_sprot.
Install/Upgrade the Taxonomy
The taxonomy has also to be (re-)generated. As user default, select the "taxonomy" databank in the DB manager and perform an upgrade in the same way as for the other databanks (select the "taxonomy" installer).
Specific cases
Upgrade Private Databanks
To upgrade the databanks that are associated with specific users, log in to Phenyx with the specific user and follow the same procedure as with a regular upgrade.
To associate a private databank to more than one user, you should edit manually the /var/phenyx/users/< user >/user.properties and and add the name of the databank to shared in the user.databanks.private= argument
