Installation by User

For the ease of their projects, users are encouraged to install software in their home directories. The following example demonstrates a typical procedure of installing the Stacks software from source. Stacks is a modular pipeline to efficiently curate and assemble large numbers of short-read sequences from multiple samples.

Given that there is a folder named ‘software’ in the user home directory the process of downloading, compiling and installing the program is the following.

• File download

> cd ~/software
> wget http://catchenlab.life.illinois.edu/stacks/source/stacks-2.4.tar.gz

• File uncompression

> tar -xvf stacks-2.4.tar.gz

• Compilation configuration. –prefix-option specifies the folder where the program will be installed to.

>  cd ~/software/stacks-2.4
> ./configure --prefix=/home/user/software

• Compilation

> make 

If no errors have occured, the installation can proceed in the software/bin folder as follows

> make install

In the software/bin directory, the user can find the binaries of the stacks pipeline.

> cd /home/user/software/bin
> ls 
clone_filter
cstacks 
gstacks
..
ustacks

Execution

> cd /home/user/software/bin
> ./ustacks

./ must always be prepended to the executable file. If ommited, then either a “no found” error will occur or a different version than the just installed one, will run.

For space saving, users are prompted to remove the compilation folder The initial compressed file could be archived for future use.

> cd ~/software
> rm -r stacks-2.4/