Bioinformatics Tools

Below are some instructions for using several bioinformatics tools on Knot.

ITSx

​ITSx can be downloaded from http://microbiology.se/software/itsx/

Simply extract the tar.gz archive and you will see the executable file called ITSx. Simply copy this executable to the bin folder in your home directory. If you don't have a folder named bin, simply create one by

mkdir bin

This folder is set up such that it is in your $PATH (you can verify by checking .bash_profile). Once ITSx is in your bin, you can simply type ITSx from the terminal to use it.

HMMER

HMMER can be downloaded from http://hmmer.org

After downloading, extract the tar.gz archive (tar -xzvf hmmer-x.x.x-linux-intel-x86_64.tar.gz), go inside the created directory and execute the following command:

./configure --prefix="/home/$USER/hmmer"

This will make sure that the executable will be installed on home folder. After this finishes, just type

make

After this finishes, perform the check

make check

This should be all OKs. Then execute

make install

Now, copy all the executables in hmmer/bin into /bin to use them from the terminal. That is

cp /home/$USER/hmmer/bin /home/$USER/bin