One of the most time-consuming and frustrating aspects of computational tasks has always been properly installing software and getting it up and running in no time. In the case of bioinformatics tools, this is notoriously difficult in some cases, particularly in Linux-based operating systems such as Ubuntu, where one-click installer files, unlike Windows, are not an option. Although much of the popular software in the bioinformatics world is easy to install in Ubuntu if one is familiar with the ecosystem, a beginner will certainly have a difficult time circling the internet trying to find a proper installation method, at least, that’s what I had to go through when I first started out.
Here in this article, I compiled out the installation methods of some of the most commonly used bioinformatics and simulation tools, as well as how to run these tools after installing them on an Ubuntu 20.04 machine. Feel free to let me know which software should be added next.
sudo apt-get -y update
sudo apt-get install -y avogadro
sudo apt-get install -y pymol
sudo apt-get install -y gromacs
cd ~ curl -k https://www.ks.uiuc.edu/Research/vmd/vmd-1.9.3/files/final/vmd-1.9.3.bin.LINUXAMD64-CUDA8-OptiX4-OSPRay111p1.opengl.tar.gz --output vmd.tar.gz mkdir -p vmd tar -xvzf vmd.tar.gz -C vmd --strip-components=1 cd vmd ./configure cd src sudo make install
sudo apt-get install -y autodock-vina
cd ~ curl -k https://ccsb.scripps.edu/download/532/ --output mgltools.tar.gz mkdir -p mgltools tar -xvzf mgltools.tar.gz -C mgltools --strip-components=1 cd mgltools bash install.sh source ./initMGLtools.sh
sudo apt-get install -y openbabel
sudo apt-get install -y openbabel-gui