SBGrid package mangager installation client

The SBGrid software stack can be installed using our CLI (command line interface) installation client for Linux (CentOS/RHEL 6 or 7 recommended) or Apple OSX computers running MacOSX v10.9 - 10.12.

Three software installers are available. Binary releases are available for MacOS and CentOS7/Ubuntu operating systems. A python release is also provided which is compatible with Mac and most Linux (CentOS6 and higher) operating systems.

The SBGrid installation client requires an individual account. To get started, first, set up an account by registering here : SBGrid registration

Pre-installation requirements

Admin access required on your computer. The SBGrid installation client will install the software tree to /opt/sbgrid and create a symlink from this directory to /programs. While admin privileges are not required to run the application, you will need admin privileges to create /opt/sbgrid and /programs .

Existing SBGrid installations must be renamed or removed. If you have previously installed SBGrid software on your computer at /programs or at /opt/sbgrid, these directories should be removed or renamed. The client will create these on first run.

Hard Drive Space Depending on what you install, ensure you have enough free hard drive space on your machine.

For large packages (Phenix, Rosetta, CCP4), a wired connection is recommended. Some packages are quite large and can be slow to download, especially over WiFi.

pip pip is a package management system used to install and manage software packages written in Python. The software installation client is installable by pip. This may not be on you machine by default, instructions for adding it are included here.

Binary releases : MacOS and Linux Installation

There is minimal installation needed for these binaries. They can be run from any location. Untar the archive, make the file executable if necessary, and run from your preferred location.

Mac : 1.0.555, 2017-06-21

Linux : 1.0.555, 2017-06-21

$ tar -zxf sbgrid-1.0.555-Darwin.tgz

$ cd sbgrid-1.0.555-Darwin

$ ./sbgrid
sbgrid <command> [<command_args>]

Available commands are:
    activate      activate new installation
    grids         list available grids
    info          print package metadata
    install       install single package
    install-all   install all packages from collection
    installed     list installed packages
    list          list available packages
    rebuild       rebuild installation
    remove        remove installed package
    resume        resume interrupted installations
    update        update package to latest release/version
    update-all    update all packages to latest release/version
    updates       list available updates for installed packages
    version       print package version string
sbgrid: error: too few arguments

Install python wheel using pip - Mac Installation

On mac, pip is available from macports, homebrew, and fink. It also can be added using easy_install. easy_install will install pip into your system python.

  $ sudo easy_install pip

Install python wheel using pip - Linux Installation

On CentOS6, you can install pip from the EPEL repository (yum -y install python-pip) or as per these directions

CLI client - Installation and activation

1. Download the latest SBGrid installation client from here.

Latest build : 1.0.555, 2017-06-21

2. Install / Upgrade with pip

$ sudo pip install SBGrid_Installer-1.0.461-py2-none-any.whl

Which should produce output similar to :

Unpacking ./SBGrid_Installer-1.0.448-py2-none-any.whl
Requirement already satisfied (use --upgrade to upgrade): pyasn1 in /nfs/programs-dev/i386-mac/python/2.7.5/lib/python2.7/site-packages (from SBGrid-Installer==1.0.488)
Downloading/unpacking requests (from SBGrid-Installer==1.0b2.dev412)
  Downloading requests-2.11.1.tar.gz (485kB): 485kB downloaded
  Running egg_info for package requests

    warning: no files found matching ''
Installing collected packages: SBGrid-Installer, requests
  Running install for requests

    warning: no files found matching ''
Successfully installed SBGrid-Installer requests
Cleaning up...

The sbgrid command will produce this usage info :

$ sbgrid
sbgrid <command> [<command_args>]

Available commands are:
    activate      Activate new installation
    list          List available packages
    info          Print package metadata
    install       Install single package
    install-all   Install all packages from collection
    installed     List installed packages
    remove        Remove installed package
    resume        Resume interrupted installations
    upgrades      List available upgrades for installed packages
    upgrade       Upgrade package to latest version
    upgrade-all   Upgrade all packages to latest version
    version       Print package version string
sbgrid: error: too few arguments

4. Activate the installation Enter your site and key which you should have received these by email.

$ sbgrid activate <site name> <user name> <activation key>

You may be prompted for your sudo password to create /programs and /opt/sbgrid.

5. On successful activation, list software titles.

$ sbgrid list

If activation continues to fail, you may have an old SBGrid installation at /programs or /opt/sbgrid. These should be removed.

You may also be blocked from accessing SBGrid servers on port 873 and port 8080 by your institution's firewall. You can check if you can access port 873 here and port 8080 here

For help, email

Installation on an external drive or USB key

Currently the installer application installs the software tree in /opt/sbgrid and uses a symlink at /programs. This link is required for the software to work, but in principle the software can be located anywhere and linked to /opt/sbgrid. This functionality is not yet included in the SBGrid application, but can be set up manually with a symlink.

An installation can be made on an external drive if you first do an install (into /opt/sbgrid), then move it and symlink to the new location.

Example: 128Gb USB 'key' drives are available on Amazon for 30$ or less and are a nice way to supplement the SSDs that come in Mac laptops. To install on an external drive like this, mount it on your computer. For this example, the mount is /Volumes/sbgrid_client_install. Then, using the SBGrid installer, do an initial installation on the hard drive. To make life easy, just do one application. Then close the installer application.

Next move /opt/sbgrid to the USB key at /Volumes/sbgrid_client_install. You will likely need sudo for this.

$ sudo mv /opt/sbgrid /Volumes/sbgrid_client_install/.

Now we have /Volumes/sbgrid_client_install/sbgrid. Create a symlink from /opt/sbgrid to /Volumes/sbgrid_client_install/sbgrid.

$ sudo ln -s /Volumes/sbgrid_client_install/sbgrid /opt/sbgrid

The symlink at /programs still points to /opt/sbgrid, and that is a link that points to the external location. Open the installer and add the desired applications. These will now install to the external drive.

Some known issues

  • rsync required on 873 or 8080. The application will fail if outbound port 873 and port 8080 are blocked by your institution or are otherwise not available.

  • Activation Failed. In some cases the Authorization dialog for admin privileges does not appear during activation. This causes the client activation to fail. This is usually due to a previously existing /programs directory or symlink from a prior installation. This must be removed for activation to be successful. Other users have reported successful activation after a restart.