Installing ATSAS

Please note that installing packages generally requires superuser (root, Administrator) privileges. Depending on your institues policies you may not be able to install the package. If unsure, please check with your local IT group before attempting an installation of ATSAS.

Please remove any existing ATSAS installations before installing a new version.

The ATSAS program suite is currently supported on three major platforms and a number of versions thereof. Please download the package for your platform and choose the appropriate installation description from the table below.

Any questions about ATSAS should be posted on the Forum.

Linux

The Linux packages for ATSAS are available for a number of distributions and architectures:

Installing and removing .deb packages (Ubuntu and Debian)

Packages are installed system-wide and the binaries are available for all users of the system equally. To install a .deb package, super-user privilidges are required. To install, download the latest package and install at the command-line with:

$ sudo dpkg --install ATSAS-X.Y.Z-1_amd64.deb

Here X.Y.Z corresponds to the current version of ATSAS. Depending on the packages already installed, an error may be printed:

dpkg: dependency problems prevent configuration of atsas:

In this case, also run:

$ sudo apt-get install --fix-broken

It is not necessary to set any environment variables after installing the .deb package. To verify the installation type:

$ dammif -v
dammif, ATSAS X.Y.Z (r....)

Verify that X.Y.Z matches the version of ATSAS previously downloaded.

To uninstall:

$ sudo apt-get remove atsas

Installing and removing .rpm packages (CentOS)

Packages are installed system-wide and the binaries are available for all users of the system equally. To install a .deb package, super-user privilidges are required. To install, download the latest package and install at the command-line with:

$ sudo yum install ATSAS-X.Y.Z-1.VERSION.x86_64.rpm

Here X.Y.Z corresponds to the current version of atsas, VERSION to the system version, e.g. el7 for CentOS-7. It is not necessary to set any environment variables after installing the .rpm package. To verify the installation type:

$ dammif -v
dammif, ATSAS X.Y.Z (r....)

Verify that X.Y.Z matches the version of ATSAS previously downloaded.

To uninstall:

$ sudo yum remove atsas

Installing and removing .run packages (all)

Installations with a graphical installer wizard are relocatable and the files may be installed anywhere in the system. Super-user priviledges may be required depending on install location. Common locations include /opt or the $HOME directory. After downloading the .run script:

• click the downloaded .run file in a file manager or start from command-line, the installer wizard starts
• follow the wizard, select the installation location and accept the licenses
• after installation, remove the .run

Note: due to the wide variety of shells and login environments on Linux, the installer wizard does not modify any login scripts to set required environment variables.

Variables that must be set manually:

• ATSAS - the installation location, e.g. /opt/ATSAS-X.Y.Z
• PATH - the location of the ATSAS binaries, e.g. /opt/ATSAS-X.Y.Z/bin

Example syntax for the common bash shell:

ATSAS=/opt/ATSAS-X.Y.Z
PATH=$ATSAS/bin:$PATH
export ATSAS PATH

Please ask your local IT department for assistance or refer to the documentation of your distribution or various online resources for a description of where and how to set the required environment variables on your system.

Be advised that required dependencies must be installed manually if not already present

Once dependencies are installed and environment variables are set, (re-)start your terminal application to include the installation directory in the search PATH to use the ATSAS command-line applications. To verify the installation, type:

$ dammif -v
dammif, ATSAS X.Y.Z (r....)

Verify that X.Y.Z matches the version of ATSAS previously downloaded.

To uninstall: open any file manager or command-line, navigate to the install directory and click or run uninstall. Manually remove the environment variables added during installation.

Installing and removing .tar.gz packages

Archives are relocatable and may be installed anywhere in the system. Whether super-user priviledges are required depends on the installation location. The .tar.gz archives are provided for the convenience of system administrators that do not want to rely on .deb/.rpm packages and possibly require a package that can be installed without a graphical user interface.

After downloading the .tar.gz archive, unpack to a target directory:

$ tar xzf ATSAS-X.Y.Z-1.*.tar.gz

Note: unpacking the archive does not modify any login scripts to set required environment variables, neither will ~/.pymolrc be modified.

Variables that must be set manually:

• ATSAS - the installation location, e.g. /opt/ATSAS-X.Y.Z
• PATH - the location of the ATSAS binaries, e.g. /opt/ATSAS-X.Y.Z/bin

Example syntax for the common bash shell:

ATSAS=/opt/ATSAS-X.Y.Z
PATH=$ATSAS/bin:$PATH
export ATSAS PATH

Please ask your local IT department for assistance or refer to the documentation of your distribution or various online resources for a description of how to set the required environment variables on your system.

Be advised that required dependencies must be installed manually if not already present

Once dependencies are installed and environment variables are set, (re-)start your terminal application to include the installation directory in the search PATH to use the ATSAS command-line applications. To verify the installation, type:

$ dammif -v
dammif, ATSAS X.Y.Z (r....)

Verify that X.Y.Z matches the version of ATSAS previously downloaded.

To uninstall: open any file manager or command-line and remove the install directory. Manually remove the environment variables added during installation.

MacOS

Installing and uninstalling .dmg packages

Installations on MacOS are relocatable and the files may be installed anywhere in the system. Common locations include /Applications/ATSAS or the $HOME directory. After downloading the .dmg disk image:

• click the downloaded .dmg file, a window opens
• click the ATSAS icon inside this window, the installer wizard starts
• follow the wizard, select the installation location and accept the license
• after installation, unmount the disk image in Finder and remove the .dmg

Note: the installer wizard modifies ~/.zprofile and defines the ATSAS environment variable and amends the application search PATH.

To use the ATSAS command-line applications, (re-)start Terminal.app to include the installation directory in the search PATH. To verify the installation type:

$ dammif -v
dammif, ATSAS X.Y.Z (r....)

Verify that X.Y.Z matches the version of ATSAS previously downloaded.

To uninstall: open Finder, navigate to the install directory and click uninstall. Do not simply remove the installation directory as this would not undo the changes done to ~/.zprofile and ~/.pymolrc.

Windows

Installing and uninstalling .exe installer wizards for the current user

Installations on Windows are relocatable and the files may be installed anywhere in the system. Common locations include C:\Program Files or the $HOME directory. Some locations may require Administrator privileges to install. After downloading the .exe:

• double click the downloaded .exe file, the installer wizard starts
• follow the wizard, select the installation location and accept the license
• after installation, remove the .exe

Note: the installer wizard defines the ATSAS environment variable, but does not modify the PATH variable. To update/modify your PATH settings:

• Open the Start menu, click Settings
• In "Find a setting", type "environment"
• Select "Edit environment variables for your account", a dialog pops up
• In the panel "User variables for ...", select "Path", click "Edit"
• Add "%ATSAS%\bin" (or the full installation directory, plus "\bin") as new entry.
• Save and close

To use the ATSAS command-line applications, (re-)start cmd.exe to include the newly modified installation directory in the search PATH. To verify the installation type:

$ dammif -v
dammif, ATSAS X.Y.Z (r....)

Verify that X.Y.Z matches the version of ATSAS previously downloaded.

To uninstall: open Explorer, navigate to the install directory and double-click uninstall.exe. Remove the ATSAS installation path manually from PATH.

Installing and uninstalling .exe installer wizards for all users

Installations on Windows are relocatable and the files may be installed anywhere in the system. Common locations include C:\Program Files or the $HOME directory. Some locations may require Administrator priviledges to install. After downloading the .exe:

To install for all users:

• open a cmd.exe terminal, navigate to the directory that contains the installer and type:

> ATSAS-X.Y.Z-1.*.exe AllUsers=true

• follow the wizard, select the installation location and accept the license
• after installation, remove the .exe

Note: the installer wizard defines the ATSAS variable in the system environment, but does not modify the PATH variable. To update/modify your PATH settings:

• Open the Start menu, click Settings
• In "Find a setting", type "environment"
• Select "Edit environment variables for your account", a dialog pops up
• In the panel "System variables", select "Path", click "Edit"
• Add "%ATSAS%\bin" (or the full installation directory, plus "\bin") as new entry.
• Save and close

To use the ATSAS command-line applications, (re-)start cmd.exe to include the newly modified installation directory in the search PATH. To verify the installation type:

$ dammif -v
dammif, ATSAS X.Y.Z (r....)

Verify that X.Y.Z matches the version of ATSAS previously downloaded.

To uninstall: open Explorer, navigate to the install directory and double-click uninstall.exe. Remove the ATSAS installation path manually from PATH.