Mascot: The trusted reference standard for protein identification by mass spectrometry for 25 years

Updating to Mascot Server 2.8

This page describes how to update your Mascot Server to version 2.8, upgrade your Mascot licence to use additional processors, and migrate a Mascot installation to new hardware. For the correct procedure, please choose from the options, below. If none of these apply, email support@matrixscience.com for more specific advice. In all cases, additional information can be found in the Mascot 2.8 Installation & Setup Manual (manual.pdf).

Towards the end of the installation, you will be asked to register your Mascot 2.8 product key to obtain a licence file. This product key is usually sent by email but may sometimes be found on a sticker on the DVD case. After successful registration, follow the link to download the licence file direct to the Mascot installation. A backup copy is sent by email.

Important: If you want to make a trial installation, do not register using your permanent Mascot 2.8 product key. Email support@matrixscience.com to request a 14 day temporary licence key.

  1. Updating Mascot Server to version 2.8 on the current hardware
  2. Upgrading Mascot Server to use additional processors on the current hardware
  3. Migrating to new hardware, optionally including an update to version 2.8 and/or an upgrade to use additional processors
  4. Additional steps for Mascot Cluster
  1. Updating Mascot Server to version 2.8 on the current hardware

     

    Linux:

    1. The update procedure is described in Chapter 2 of the Installation & Setup Manual.
    2. The installation script will update mascot.dat by adding new options, but will retain all existing sequence database configuration settings and other options.

    Windows:

    1. Do not uninstall the old version of Mascot. Just run the 64-bit setup as described in Chapter 3 of the Installation & Setup Manual.
    2. If a configuration file from the previous version of Mascot is to be replaced, it will be moved to a folder under the main Mascot folder called _install_backup.

  2. Upgrading Mascot Server to use additional processors on the current hardware

     

    1. After registering your new product key and downloading the licence file, go to the Database Status page and verify that the number of processors shows the correct, new value.
    2. The number of threads displayed for each active database should be -1, which means this setting is auto-determined. If the number of threads for a database has been specified as a fixed number, you may or may not wish to change this in view of having more processors available (Configuration Editor; Database Manager).

  3. Migrating to new hardware, optionally including an update to version 2.8 and/or an upgrade to use additional processors

     

    To migrate to new hardware without any update or upgrade, contact support@matrixscience.com to request a new product key, in advance.

    If you do not wish to transfer your old searches, skip steps 4 – 6

    1. Perform a clean installation of Mascot on the new system by following the instructions in Chapter 2 (Linux) or Chapter 3 (Windows) of the Installation & Setup Manual.
    2. If updating from Mascot 2.3 or earlier, towards the end of the installation, before trying to register your 2.8 product key, copy your old licence file to the Mascot config directory on the new server (this is a small text file called mascot.license in the Mascot config directory on the old server).
    3. Ensure everything is working correctly. Run a couple of test searches from a web browser on a different PC and make sure you can view the result reports.
    4. Copy all your search result files from the old system. That is, all the "daily" directories, such as 20120630, in mascot/data. Do not copy mascot/data/test, mascot/data/cache, or the files in mascot/data itself.
    5. Copy over mascot/data/mascot.job, replacing the file on the new system (this file contains the last job number).
    6. Copy over the search log (mascot/logs/searches.log), replacing the file on the new system. Check you can open old search results using the links in the search log.
    7. If Mascot security was enabled on the old system, copy across mascot/config/security_options.xml, group.xml, and user.xml.
    8. Other files in mascot/config that you may have modified are crosslinking.xml, enzymes, fragmentation_rules, library_mod_aliases, quantitation.xml and taxonomy. Best to use diff (Linux) or fc (Windows) to compare the old and new versions before copying any old configuration files to the new system.
    9. To migrate custom modifications from a server running Mascot 2.5 or later, copy across mascot/config/unimod/usermod.xml. If the old server is Mascot 2.7 or later, also copy across mascot/config/unimod/usermod_xl.xml. If the old server is Mascot 2.4 or earlier, see the note under Known Issues on this page.
    10. The sequence database migration procedure is described on this page.
    11. Mascot must then be deleted or uninstalled from the old system.

  4. Additional steps for a Mascot Cluster

     

    The above procedures also apply to the master node of a Mascot Cluster. For an upgrade to use additional processors in a cluster:

    1. Stop the Mascot Service (Windows) or kill ms-monitor.exe (Linux).
    2. In the cluster section of mascot.dat, the number of processors in SubClusterSet 0 should be set to -1 (automatic). If it is a fixed number, you will need to change this to -1 or to the new number of processors.
    3. Edit nodelist.txt to change the numbers of processors on existing search nodes and/or add new definitions for additional search nodes.
    4. The operating system on each new search node must be configured exactly as described in Chapter 11 of the Installation & Setup Manual.
    5. Start the Mascot Service (Windows) or start ms-monitor.exe (Linux).