Installation with Docker
To offer a complete solution for data mining, tree inference and dating etc, the SUPERSMART pipeline ships with a variety of high-end third-party phylogenetic software tools. To prevent users from having to install all these tools as a prerequisite, SUPERSMART runs as a virtual research environment, powered by Docker. This ensures an easy installation with just a few clicks or commands. Here we give detailed installation instructions for different operating systems.
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Download and install Kitematic, the graphical user interface for running Docker apps.
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Open Kitematic and you will see several software tools available for download (Kitematic looks somewhat similar to an app store). In the search field at the top of the window, enter supersmart:
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Click on Create to download SUPERSMART. Note that several gigabytes will be downloaded, so this may take a while.
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You can now see SUPERSMART in the Containers panel on the left hand. Select the SUPERSMART container and click on the Exec symbol in the top panel to start the SUPERSMART environment:
This will open a terminal window in which the virtual environment is running.
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Now the commands
smrt,smrt-configandsmrt utilsare available in the terminal.smrt --helpwill give you an overview of subcommands available. For information on how to use the SUPERSMART commands, please refer to the analysis-run-through and to the examples. -
Files created within the
/shared/directory on the SUPERSMART virtual research environment (i.e. the Docker virtual machine), can be accessed from your computer. To specify the directory which maps to the/shared/directory on the virtual host, select on Settings -> Volumes in the right panel in Kitematic, and then click change. A file dialog will let you chose a folder which is the interface to the SUPERSMART environment.