1. Home
  2. Docs
  3. Software
  4. Installation by User

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 


> 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/