1.3 Software used during this tutorial

Commands will be issued within a “Text Terminal”:

Macintosh: Terminal located in /Applications/Utilities
Windows: Terminal from “Windows Subsystem for Linux” (see above.)
Linux: Terminal icon might be called “shell.”

The following software can be installed or can alternatively be used within docker (see below.)

EMBOSS - http://emboss.sourceforge.net/
Clustal Omega - http://www.clustal.org/omega/
TCoffee - http://www.tcoffee.org/

docker users have the alternate option to download images rather than install software:

docker - https://docs.docker.com/get-docker/ (free registration required.)
docker images used for:
- EMBOSS: https://hub.docker.com/r/pegi3s/emboss
- Clustal Omega: https://hub.docker.com/r/pegi3s/clustalomega
- TCoffee: https://hub.docker.com/r/cbcrg/tcoffee

pegi3s: Bioinformatics Docker Images Project: https://pegi3s.github.io/dockerfiles/

cbcrg: Comparative Bioinformatics Centro de Regulacio Genomica (Center for Genomic Regulation) - (Barcelona): https://hub.docker.com/u/cbcrg

Readers can pre-download the docker images with the following commands, assuming that docker has been installed.

# login 
docker login # may not be necessary

# "Pull" the images with the docker pull commands that follow:

docker pull pegi3s/emboss:latest

docker pull pegi3s/clustalomega:latest

docker pull cbcrg/tcoffee

Note: These commands can be found on the Docker Hub for each image under the “Tags” tab.

1.3.1 A note about Docker

The docker software is a wonderful tool to be able to run Linux software that does not need to be installed on the local, host computer. docker images are used to create a container that will run the software independently of the operating system of the host computer. Even though the software is Linux it can run on Macintosh and Windows as well within the container.

However there are limitations to being able to use that software:

The CPU has to be new enough to possess “Hyper-V” virtualization architechture. Therefore older computers cannot take advantage of this technology.
There are many images available on the “docker hub” but many of them do not offer clear instructions and may not be useable by everyone.

In this tutorial I have used images that are functional for the purpose at hand, and I have supplied the complete commands to run both the container but also the software within. Therefore the reader only need to install the docker software to use this option. Alternatively, all commands used within a container would transpose exactly if the used software were to be installed on the local computer.