INSTALL.txt

INSTALL

Install bowtie and bowtie2 into a directory, which is included in the computers PATH search variable.
Such as /usr/bin/ or /usr/local/bin.

cld is installed by copying the cld binary to the path of choice. 
We recommend /usr/bin or /usr/local/bin as these paths are usually 
already included in the computers PATH search variable.

unzip cld-master.zip

cd cld-master

cd cld-your-system/

sudo cp cld /usr/bin/

OR is you are working already under Linux just:

cd cld-master

sudo cp cld /usr/bin/

Added the custom interval tree Package for fast build and access to rebuild interval trees. 
Install it via "perl Makefile.PL"; "make" ; "sudo make install" from Set-intervalTree. 
All other dependencies of CLD are available online at CPAN.

After successful installation, calling cld directly from the command line can start 
cld, only requirement are rights to read and write from the input and 
output directories passed to cld.

For further information look at README