Installation and Platform Notes

Licenses

A license file from OpenEye Scientific Software is required to run any OpenEye application. A license file can be requested/obtained by contacting OpenEye at business@eyesopen.com.

At startup, the application looks for a valid license in the following default locations:

  • In a file specified by the environment variable OE_LICENSE.

  • In a file named oe_license.txt in the directory specified by the environment variable OE_DIR.

  • In a file named oe_license.txt in the user’s platform-specific local OpenEye application data directory. The location of this directory is detailed below:

    • Linux/UNIX:

      ~USERNAME/.OpenEye

    • Mac OS X:

      /Users/USERNAME/Library/OpenEye

    • Microsoft Windows Vista/7/8:

      C:\Users\USERNAME\AppData\Local\OpenEye

  • In a file named oe_license.txt in the current working directory

If a valid license is not found in one of the default locations, the user will be prompted to specify the location of the license file. The user may specify a local file, a file on a network/shared drive, or a network URL. If the specified file contains a valid license, the license file will be copied to a local cache so that it does not have to be found each time.

When the license file expires, a new license will automatically be searched for in the location that was specified for the current license. If a valid license is found in that location, it will automatically by copied over and used without any user action required. If a valid license file cannot be found, the user will again be prompted to locate one. When there are fewer than 30 days remaining on the current license, the application title bar will change to report the number of days remaining.

Once VIDA has started, the user can view the actual license file being used (i.e. the locally cached copy), specify a new license file, or force an update of the current license from the originally specified location. These options can be accessed in the License submenu of the main Help menu.

Installation

Linux

Linux distributions are provided as a gzipped tarball of the distribution tree described below. Installation is performed by simply untarring the file in the desired location. The top-level directory in the tarball is named openeye. Distributions for different Linux variants can be installed into the same location, allowing multiple Linux versions to be run from a single shared directory.

To ensure that the installed applications can be called from the command line, be sure to add the full path of the openeye/bin subdirectory to the PATH environment variable. For instance, if the distribution was installed into /usr/local/openeye, the PATH environment variable should contain: /usr/local/openeye/bin.

Under the top-level openeye directory are the following subdirectories:

arch:This directory contains the collection of platform specific subdirectories. Each subdirectory contains the actual installed executables and support libraries for the associated platform. In the platform specific subdirectory there will be a subdirectory for each application. Within that will be another subdirectory for each version of that application.
bin:This directory contains a startup script for each application that has been installed. This script determines, at run-time, what the current platform is and then calls the appropriate executable in the arch. This script enables the easy co-existence of multiple platforms and versions of any OpenEye application in the same distribution tree.
data:This directory contains all of the associated data for the installed applications. There will be a subdirectory for each installed application and within that subdirectory there will be another subdirectory for each specific version of that application.
docs:This directory contains all of the documentation associated with the installed applications. There will be a subdirectory for each installed application and within that subdirectory there will be another subdirectory for each specific version of that application.
examples:This directory contains all of the examples associated with the installed applications. There will be a subdirectory for each installed application and within that subdirectory there will be another subdirectory for each specific version of that application.

The startup script discussed in the section on the bin directory above will have the same name as the installed executable with which it is associated. When the script is called, it will attempt to determine the current platform and run the appropriate executable if installed. If an appropriate executable cannot be found, the script will report that information, as well as a list of the currently installed platforms. The auto-detection can be overridden by setting one of two environment variables:

  • OE_ARCH can be used to specify a colon separated list of compatible distributions for the current platform such as:

    redhat-RHEL6-x64:redhat-RHEL5-x64

    Specification of this environment variable overrides the auto-detection process, if it is present. If none of the compatible distributions listed are found, the script will fall back to the auto-detection process.

  • APPNAME_OE_ARCH can be used to specify a colon separated list of compatible distributions for a specific application (as specified by changing the APPNAME text in the environment variable name) just like OE_ARCH as detailed above.

    Specification of this environment variable overrides the OE_ARCH environment variable as well as the auto-detection process. If none of the compatible distributions listed are found, the script will fall back to the OE_ARCH list first and then to the auto-detection process.

    Specifying this variable provides a simple way to customize the behavior for individual applications on non-standard platforms.

The startup script also supports a few commandline arguments including:

-path Specifying this argument will output the full path of the executable to be run. The executable will not be started if this argument is present.
-print_arch Specifying this argument will output the details of the current platform as detected by the script as well as which platform-version of the executable is being run. The executable will be started if this argument is present.
-use_version Specifying this argument followed by a specific version number allows the user to control which released version of the executable to run.

Windows

Windows distributions are provided as a standard EXE installer. For installation double click the executable and follow the installation instructions. By default, OpenEye applications will install into the C:\Program Files (x86) directory (for 32-bit applications) or C:\Program Files (for 64-bit applications).

Under the application directory (C:\Program Files\Application Name) there are subdirectories for:

bin:This directory contains the application executable.
data:This directory contains all of the associated data for the installed applications.
docs:This directory contains all of the documentation associated with the installed applications.
examples:This directory contains all of the examples associated with the installed applications.

An OpenEye group with an application specific subgroup will be added to the Start menu. The application specific subgroup will contain links to the documentation, the uninstaller, and, for some applications, a Windows command shell with PATH settings already defined to allow the user to simply type the executable name at the prompt without concern for where the executable is actually installed. Links are also included to add and remove the installed location to the user’s default path.

For graphical applications, a link to the application will be created on the desktop as well as in the application specific subgroup of the Start menu.

Mac OS X

Mac OS X distributions are provided as a dmg disk image. For installation, double click the .dmg file to open it, and drag the application to the Applications folder.

A folder containing documentation and example data is included in the disk image (Right click, Show Package Contents). Under the top level Contents folder there are subdirectories for:

data:This directory contains all of the associated data for the installed applications.
docs:This directory contains all of the documentation associated with the installed applications.
MacOS/bin:This directory contains the application executable.

The documentation and example data can be copied to any convenient location. Graphical applications have built-in documentation, which is available from the application’s Help menu.

For command-line only tools, an application named “Install Command Line Support” can be run from the .dmg file, and this will allow the user to add the application’s location to the user’s PATH environment variable. Command-line applications can also be run from the Applications folder, in which case they will open a terminal window with a properly configured environment.

Enterprise Installation for Windows

It is possible to perform a “silent installation” of VIDA by running the installer with the /S flag. During a silent installation, no progress or other installation windows will be displayed. If this flag is used, the installer should be run from an administrative account to avoid the appearance of a “User Account Control” dialog during installation. No reboot is required after installation.

By default, the OpenEye file extensions “.oes” (VIDA state files), “.oeb” (OpenEye binary files), and “.vpy” (VIDA Python scripts) are associated with the VIDA application. Users can optionally associate Mol files (.mol, .sdf, .sd), PDB files (.pdb, .ent), Mol2 files (.mol2), and grid and surface files (.grd, .agd, .srf, .oesrf) with VIDA, but by default these optional associations are not made.

Removal

Linux

To uninstall a single distribution of a product the relevant subdirectories for that product and version simply need to be deleted from within the following directories:

arch:In the openeye/arch directory is a platform specific subdirectory. Within this are directories for each installed product and within those are subdirectories for each version of the product. Delete the subdirectory for the version which is to be uninstalled. For example, to delete or uninstall v1.0.0 of a product, delete the folder “<product_name>/1.0.0”.
data:In the openeye/data directory is a subdirectory for each installed product and within those are subdirectories for each version of the product. Delete the subdirectory for the version which is to be uninstalled.
docs:In the openeye/docs directory is a subdirectory for each installed product and within those are subdirectories for each version of the product. Delete the subdirectory for the version which is to be uninstalled.
examples:In the openeye/examples directory is a subdirectory for each installed product and within those are subdirectories for each version of the product. Delete the subdirectory for the version which is to be uninstalled.

Windows

OpenEye applications can be uninstalled through the Windows Control Panel. Open the Control Panel and select Programs and features, then select the application and click Uninstall.

For graphical applications, uninstallation also removes the application’s link from the desktop and Start menu.

Mac OS X

To uninstall a single distribution of an application simply drag the application from the Application folder to the Trash.

Some applications may, at the user’s request, install symbolic links in the /usr/local/bin directory, and modify the PATH variable in the .openeyerc.* file(s) in the user’s home directory. The symbolic links may be safely deleted after uninstallation, and the .openeyerc.* file(s) can be edited, if desired, to remove obsolete entries.

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