Problem installing RATT

Question

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.

Answer 1

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.