The following libraries are necessary to successfully compile RNAmotif:

• bison
• byacc
• flex

% sudo apt-get -y install bison byacc flex

Here is the procedure to install RNAMotif from its source code:

• The archive has been downloaded from the web in /home/bioubuntu, decompressed and the newly created folder moved into /opt/bio/sources.

• This folder should belong to root and its permissions should be set to 755.

% sudo chown -R root:root /opt/bio/sources/rnamotif-3.0.5

• Once you are in /opt/bio/sources/rnamotif-3.0.5, compilation is easily done:

% sudo mkdir bin 
% cd ./src
% sudo make 

• After compilation, I move the executables in /opt/bio/sources/rnamotif-3.0.5/bin:

% find . -perm 755
// You will get a list
// of executables
% sudo mv <item> ../bin

• To make sure everyone has access to the programs, I modified the /etc/profile file by adding these lines:

#
# RNAMotif specific environment variable
#
PATH=/opt/bio/sources/rnamotif-3.0.5/bin:$PATH
EFNDATA=/opt/bio/sources/rnamotif-3.0.5/efndata