# Pre-installed Linux tools

{% hint style="info" %}
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](/working-in-the-sandbox/which-tools-are-available/lmod-linux-tools.md). Before using the terminal window, we recommend that you [familiarize yourself first with Linux](/background-reading/how-to-get-started-with-unix.md).
{% endhint %}

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.`

{% hint style="info" %}
If you would like new programs to be included in the Sandbox, please contact <humgen-servicedesk@helsinki.fi>.
{% endhint %}

{% hint style="warning" %}
In the future, existing and new FinnGen-specific programs will be executed using [Lmod](/working-in-the-sandbox/which-tools-are-available/lmod-linux-tools.md).
{% endhint %}

### 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.

![](/files/SuryZenHDFebuqfmLxry)

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:

![](https://lh4.googleusercontent.com/Zh-gwLrrVRPhsuvYpNjmdqAwMWJjYBmDisBeobimW5TEa0wCPh18lEpnfsMQ3T_AA7VUKhMT12RNcXmTUPhW2QosgfT8JWgOpEV9jbokRpwm_lq2lMZbWLZn3AnlLjhQN-c8sK7r=s0)

![](https://lh5.googleusercontent.com/9jYoQL5WrlfjdciZBPsA87Y1QUJABUGbkozwv3XhrwBFtJSU2pcKcGMutvReJeguZZxKr6WRKTzZmFqOH1bydKiLrMkmFwB6e-VvkywsJw6-cLuv9zsfLXLDhIOgSJbp5PFngA6R=s0)

![](https://lh6.googleusercontent.com/nw6K1dU2jrJd-u2kaB4yLTLMCU5boqJtJFR4Xq7LdYsZDNos5oLJQY1745gpH0G8n9hQiEUlUWNxwqlNKpTR1jlhG1dBFAMMJ6eIwVhLqhZ96eKgTzTUyBR6LFLw6vVgDsFbD0W-=s0)


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