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
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
> 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/