BDG Installation Manual   next
Chapter 0

Description of the installation manual

Copyright    © 1999-2006 by Global Phasing Limited
 
  All rights reserved.
 
  This software is proprietary to and embodies the confidential technology of Global Phasing Limited (GPhL). Possession, use, duplication or dissemination of the software is authorised only pursuant to a valid written licence from GPhL.
 
Contact buster-develop@GlobalPhasing.com
sharp-develop@GlobalPhasing.com


Contents

This manual describes how to install BUSTER-TNT or SHARP/autoSHARP, software systems for crystallographic structure determination and refinement by Bayesian statistical methods. The submission of BUSTER-TNT or SHARP/autoSHARP jobs in a multi-machines environment with a queueing system is also described. Since BUSTER-TNT and SHARP/autoSHARP share most of the underlying infrastructure, the two names are used synonymously throughout this document. If there are differences between the two, it will be mentioned explicitly.

The installation manual is available online for BUSTER-TNT and SHARP/autoSHARP. A very short installation description is given below.

This document does not deal with the input preparation or the output of the BUSTER-TNT and SHARP/autoSHARP programs themselves. For more information about these please refer to the on-line documentation.

The manual consists of six chapters:

There is also a list of frequently asked questions (FAQ) available. Although it is rather directed towards problems that a user of the programs might encounter, it also offers some hints about administration. Furthermore, you can have a look at the online FAQs hosted on the SHARP/autoSHARP home page.


Installation in a nutshell

The BUSTER/SHARP administrator needs to take the following steps to install and configure SHARP/autoSHARP and/or BUSTER-TNT:

  1. Select the machine which will be the SERVER for BUFFET/SUSHI (graphical user interfaces, GUIs, to BUSTER-TNT and SHARP/autoSHARP respectively). This machine will run a HTTP demon. This machine must be able to run CCP4 and Perl.

  2. Decide under which UNIX account the software should be installed. It is not recommended to install and/or run the software using the root account. Rather, either a normal user account or the standard account for installing crystallographic software should be used.

    Note : if running jobs through the GUI, all output files will belong to this UNIX account (i.e. UNIX ownership of all files produced during a job).

  3. From this machine and account, download SHARP/autoSHARP and/or BUSTER-TNT, the corresponding tutorials, the helper applications (and TNT if you run BUSTER) as well as the installation script into a clean directory (known as $BDG_home). These downloads are available from our WWW pages at http://www.globalphasing.com/sharp/ and http://www.globalphasing.com/buster/ (a message with access information was sent to you when your initial licence request was processed).

  4. For each machine which will run the actual BUSTER-TNT or SHARP/autoSHARP programs (a so-called MASTER machine) you will need a licence key. These (additional) licence keys can be requested from our WWW page and are tied to a specific initial licence request. All these licence keys are then stored in a single file .licence in the $BDG_home directory (please note the spelling of this file).

  5. Run the installation script (GPhL_SHARP_install.sh or GPhL_BUSTER_install.sh):

    During sections 1 to 5 of this script, it will install the various parts of the software. In section 6, it will configure the installation. Make sure it runs successfully till the end.

    If you've run the script with the -F flag, you should be finished now - unless you want to use more than just the current machine.

    If you run it without any flag, the SERVER (i.e. the GUI-driving http daemon) is configured, but the actual SHARP/autoSHARP or BUSTER/TNT programs cannot run yet.

    Make sure to set some environmental variables: example scripts (which should be correct) are provided as setup.sh and setup.csh in the current $BDG_home directory after running the installation script. You can set up your environment using

          # . ./setup.sh                # for sh/bash/ksh
            - or -
          % source ./setup.csh          # for csh/tcsh
          

  6. Each MASTER machine needs to be configured using the $BDG_home/adm/bin/newmachine script. Now the system is fully operational, but nobody can use it yet.

  7. The path to various helper programs need to be known to the installation through the script $BDG_home/bin/helpers.local (see also the file $BDG_home/bin/helpers.local_template). This is only needed when viewing results directly through the GUI. Now the connection from the GUI to the viewer applications is set up.

  8. The BUSTER-TNT and/or SHARP/autoSHARP users need to be added to the database, using the $BDG_home/adm/bin/newuser script. This script sends an e-mail to the users instructing them about the last configuration step (if the mail system doesn't work correctly, any email is also saved in $BDG_home/users/<user name>).

    Each SHARP/autoSHARP user runs from their account a final configuration script ($BDG_home/bin/useSHARP), which completes the configuration. The corresponding step for BUSTER-TNT is done differently and takes place during the initial connection to the BUSTER server.


Last modification: 15.05.09