DivCon Discovery Suite Installation

DivCon Discovery Suite Installation

1. Prerequisites and basic installation instructions:

  • If you need access to the software installation package, contact sales@quantumbioinc.com for information and download instructions. If you attempt to run the software and have any difficulty, email support@quantumbioinc.com for additional information.
  • Platform Support:
    • Linux_x86: The primary distributions include CentOS/RHEL 5 and CentOS/RHEL 6, and the software is also regularly tested on newer versions of Fedora, Ubuntu, etc.
    • Mac OS X 64bit: The build for Mac OS X is built on Mac OS X v10.7.5 and should therefore run on any 64bit OS version which has come out since.
  • Use of PHENIX/DivCon requires the installation of both the DivCon Discovery Suite as noted in the general Suite manual and the installation of a version of Phenix which has the proper “hooks” available. These hooks have been in place in Phenix versions since phenix-dev-1525. To install phenix, download a newer version of Phenix and follow the standard Phenix installation instructions. Note: it is highly recommended that you install Phenix 1.10 or later. Also, in our experience, the “dev” (or nightly build) versions of Phenix intermittently break any number of hooks and options. If you run into any trouble with a dev version, please shift to a newer/different version.
  • If you wish to use MOE/DivCon plugins, you will need to run MOE2016 or newer. Please contact CCG for information and instructions.
  • The package contains most of the 3rd party software used by the Suite; however, some basic system libraries are also be required. In most cases, these packages will already be installed on your system, but if you see errors that certain *.so files are missing when you try to run qmechanic, then your administrator may need to install some of them for you. The following line will install this software on a yum-based distribution. Other distributions will have similar package management facilities.
    • CentOS, Fedora, Amazon Linux, and other yum-based distributions: 
      sudo yum install bzip2-libs.x86_64 glibc.x86_64 keyutils-libs.x86_64 jq.x86_64 \   
    krb5-libs.x86_64 libcom_err.x86_64 libselinux.x86_64 openssl098e.x86_64 bc bash perl gzip
    • Ubuntu, Debian, and other apt-get -based distributions (note: the 32bit ia32-libs libs are only required to run the installer. The “tar-ball” installer can be used to circumvent this requirement): 
      sudo apt-get install ia32-libs bc bzip2 libc keyutils krb5-kdc bash openssl perl gzip jq
  • To install the DivCon Discovery Suite, download the package from the link provided (email sales@quantumbioinc.com to request a download link) and run the installer. You may install the software in your own directory and administrator privileges are not required. Both an installer image and a tar-ball image are available and the software may be installed using any of these steps:
    • Option #1 (Installer – Linux): 
      chmod +x DivConDiscoverySuite-b####-linux-installer.bin
./DivConDiscoverySuite-b####-linux-installer.bin
    • Option #2 (Installer – Mac): 
      tar zxvf DivConDiscoverySuite-b####-osx-installer.app.tar.gz
open DivConDiscoverySuite-b####-osx-installer.app
    • Option #3 (Installer – cross-platform tar ball on either Mac or Linux): 
      tar zxvf DivConDiscoverySuite-b####.tar.gz

      Please NOTE: For Option #3, if you wish to use CSH/TCSH, then you will need to update the QBHOME environment variable found on line 6 of the /path/to/DivConDiscoverySuite/etc/qbenv.csh file by replacing the IN_INSTALLDIR string to match the root path to your installation.

  • Temporary Note for macOS Users: In order to execute command line tools with newer versions of the macOS, you will need to execute the following command line options. This requirement will be addressed in an upcoming version of the DivCon Discovery Suite: 
    xattr -d com.apple.quarantine /path/to/DivConSuite-bXXXX/darwin-i386/bin/* 
xattr -d com.apple.quarantine /path/to/DivConSuite-bXXXX/darwin-i386/lib/*
  • To install the license file, if you don’t already have a license file, request one from sales@quantumbioinc.com then copy the file into the package etc/ directory (be sure the name the file “license”). 
    gunzip provided_license_file.gz
cp provided_license_file /path/to/DivConDiscoverySuite-b####/etc/license

2. Install QuantumBio-supplied plugins to MOE from CCG

The DivCon Discovery Suite includes SVL files within the svl directory to extend the functionality of MOE and MOE/batch specifically for X-ray refinement. To install this plugin, use the following steps:

  • Option #1: For system-wide installation of the QuantumBio MOE menu, add the following line to the end of the $MOE/lib/moe-menus file:include “/path/to/DivConSuite-bXXXX/moe-menus”
  • Option #2: Or for user-specific installation of the QuantumBio MOE menu, add the following line to the end of the $HOME/moe-menus file (create this file if it does not exist):include “/path/to/DivConSuite-bXXXX/moe-menus”
  • Make sure the MOE bin directory is in your path so that it will be picked up by the execution script.export PATH=/path/to/MOE####/bin:${PATH} # for sh/bash
    setenv PATH /path/to/MOE####/bin:${PATH} # for csh/tcsh
  • For MOE2015, with the QuantumBio-provided SVL files can be loaded and run using the following on the command line: 
    /path/to/DivConSuite-bXXXX/bin/qbmoe     # to start MOE GUI 
/path/to/DivConSuite-bXXXX/bin/qbmoebatch    # to start MOE/batch command line
  • For MOE2016 and newer, CCG removed the MOE_SVL_LOAD environment variable and it is no longer used. Therefore, you must perform the following steps within your home directory:For MOE2016 and newer, CCG removed the MOE_SVL_LOAD environment variable and it is no longer used. Therefore, you must perform the following steps within your home directory: 
    mkdir -p $HOME/moefiles/svl # create local MOE system directories.
cd $HOME/moefiles/svl ; ln -s /path/to/DivConSuite-bXXXX/svl qb.svl # create symbolic link to supplied SVL

    Note: going forward, you must keep this link updated for each package distribution provided by QuantumBio. Each time QuantumBio distributes a new package and your organization installs it, you must update this link to the new DivConSuite-bXXXX/svl directory.

 

Once the package is installed, you can run some tests to make sure all is in order. The following tutorials and examples are available depending upon your goals:

If you run into any difficulty with the installation or execuation of any tools within the DivCon6 Suite, please Contact Us immediatelly – we are happy to help!

Updating Previous Install

If there is a previous install of the DivCon Discovery Suite, the new installer will install the new version in a separate directory. The old $QBHOME/etc/license file needs to be moved to the new $QBHOME/etc/ directory and the above noted new moe-menus file should be placed over the old moe-menus file within the $HOME directory. Once the new install has been tested within your environment, the old install may be deleted.

DivCon Discovery Suite Contents