<p>Usually the home of a program is where the executable is. In order to make the system aware you need to include it as a variable when the terminal is run.</p>

<p>So you need to add it to the file at <code>~/.bashrc</code> of your computer (if you are using bash as shell [you can check it with <code>echo $SHELL</code>]). You need to add :</p>

<pre><code>export RATT_HOME=path/where/RATT/is/installed/or/downloaded
</code></pre>

<p>As terdon says in a comment below:</p>

<blockquote>
  <p>Note that echo <code>$SHELL</code> just prints the default login shell of the
  user, and not necessarily the shell that is currently running.  Also,
  <code>~/.bashrc</code> is not read by macOS bash which starts login shells by
  default. In any case, this sort of global variable should be in
  <code>~/.profile</code>, not <code>.bashrc</code>. For more of this sort of detail see
  <a href="https://askubuntu.com/questions/463462/sequence-of-scripts-sourced-upon-login/463479#463479">Sequence of scripts sourced upon login</a> and <a href="https://unix.stackexchange.com/questions/26047/how-to-correctly-add-a-path-to-path/26059#26059">How to correctly add
  a path to PATH</a>.</p>
</blockquote>

CC BY-SA 3.0
2018-01-25T19:13:27.113Z
2018-01-25T19:26:10.780Z
2018-01-25T19:26:10.780Z
llrs
<p>I have followed the steps <a href="http://ratt.sourceforge.net/" rel="nofollow noreferrer">here</a> to install RATT, i.e.:</p>

<pre><code>svn co "https://svn.code.sf.net/p/ratt/code/" ratt-code
</code></pre>

<p>However, when I check my installation by running '$RATT_HOME/start.ratt.sh', it says:</p>

<pre><code>zsh: no such file or directory: /start.ratt.sh
</code></pre>

<p>which makes sense once I check that the RATT_HOME variable is empty.</p>

<p>I downloaded their tuberculosis example, went into that directory and ran: </p>

<pre><code>~/path/to/my/ratt/ratt-code/start.ratt.sh embl F11.fasta F11 SimStrain
</code></pre>

<p>and got the following output:</p>

<pre><code>Please set the RATT_HOME variable.
At Sanger for bash it is RATT_HOME=/nfs/users/nfs_t/tdo/Bin/ratt; export RATT_HOME
At Sanger for tcsh setenv RATT_HOME /nfs/users/nfs_t/tdo/Bin/
</code></pre>

<p>What should I set my RATT_HOME variable to? The message only says what it should be set to at the Sanger Institute.</p>

<software-installation><sequence-annotation><functional-annotation><ratt>
Problem installing RATT
# Problem installing RATT

(Asked by: username_0 on 2018-01-25)

I have followed the steps here to install RATT, i.e.:
svn co "https://svn.code.sf.net/p/ratt/code/" ratt-code

However, when I check my installation by running '$RATT_HOME/start.ratt.sh', it says:
zsh: no such file or directory: /start.ratt.sh

which makes sense once I check that the RATT_HOME variable is empty.
I downloaded their tuberculosis example, went into that directory and ran: 
~/path/to/my/ratt/ratt-code/start.ratt.sh embl F11.fasta F11 SimStrain

and got the following output:
Please set the RATT_HOME variable.
At Sanger for bash it is RATT_HOME=/nfs/users/nfs_t/tdo/Bin/ratt; export RATT_HOME
At Sanger for tcsh setenv RATT_HOME /nfs/users/nfs_t/tdo/Bin/

What should I set my RATT_HOME variable to? The message only says what it should be set to at the Sanger Institute.

**Tags:** software-installation, sequence-annotation, functional-annotation, ratt

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## 1 answers

### Answer by username_1 on 2018-01-25. Score: 3 | Accepted answer

Usually the home of a program is where the executable is. In order to make the system aware you need to include it as a variable when the terminal is run.
So you need to add it to the file at ~/.bashrc of your computer (if you are using bash as shell [you can check it with echo $SHELL]). You need to add :
export RATT_HOME=path/where/RATT/is/installed/or/downloaded

As terdon says in a comment below:

Note that echo $SHELL just prints the default login shell of the
  user, and not necessarily the shell that is currently running.  Also,
  ~/.bashrc is not read by macOS bash which starts login shells by
  default. In any case, this sort of global variable should be in
  ~/.profile, not .bashrc. For more of this sort of detail see
  Sequence of scripts sourced upon login and How to correctly add
  a path to PATH.


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