Pre-installed Linux tools

Users of the FinnGen sandbox can use the IVM Virtual Machine (IVM) terminal window to execute pre-installed Linux programs. Other FinnGen-specific Linux programs can be loaded using Lmod. Before using the terminal window, we recommend that you familiarize yourself first with Linux.

The IVM Virtual Machine (IVM) terminal window can be used to execute Linux programs pre-installed in the following directories:

/usr/bin/

/usr/local/bin/

• The first directory contains basic Linux tools such as awk and grep.

• The second directory contains FinnGen-specific tools such as PRSice, plink and eigenstrat.

If you would like new programs to be included in the Sandbox, please contact [email protected].

In the future, existing and new FinnGen-specific programs will be executed using Lmod.

Finding pre-installed Linux tools

• You can use the which command to find out if a program has been pre-installed.

or

• You can use the ls /usr/bin/ and ls /usr/local/bin/ commands to list all programs that have been pre-installed in these directories.

In the example below, we used the which plink command to confirm that this program is pre-installed. The which returned the directory location where the program is installed. If the program is not installed then no location is returned.

In the example below, we used the ls /usr/local/bin/ command to list all pre-installed FinnGen-specific tools. Please note that only some of the programs are shown below and that the listing is from the year 2021: