Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 3.0
Answers.CreationDate: 2018-01-25T19:13:27.113Z
Answers.LastActivityDate: 2018-01-25T19:26:10.780Z
Answers.LastEditDate: 2018-01-25T19:26:10.780Z
Answers.UserDisplayName: llrs
Body: <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>
  
Tags: <software-installation><sequence-annotation><functional-annotation><ratt>
Title: Problem installing RATT
ThreadText: # Problem installing RATT
  
  (Asked by: username_0 on 2018-01-25)
  
  I have followed the steps [here](http://ratt.sourceforge.net/) 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
  
  
  ---
  
  ## 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](https://askubuntu.com/questions/463462/sequence-of-scripts-sourced-upon-login/463479#463479) and [How to correctly add
  > a path to PATH](https://unix.stackexchange.com/questions/26047/how-to-correctly-add-a-path-to-path/26059#26059).
  
  
  ---
  
  