bioinfomed

This tutorial required:

• a computer (under Linux, Mac, Windows) with an internet connection

• To know what a fasta or fastq (fastaq = fq) file is

• an access to a Galaxy website server, including usual tools for metagenomic analysis

See what is the Galaxy project: Wikipedia or Official website

Example of the main display page of Galaxy (using a browser)

⇒ 3 possibilities to get access to a Galaxy server:

1) Use a free distant server

Many public Galaxy servers are available. Here a list of servers including the required metaG tools (list updated November 2022):

https://africa.usegalaxy.eu/
https://india.usegalaxy.eu/
https://ecology.usegalaxy.eu/
https://galaxy.genouest.org/
https://metagenomics.usegalaxy.eu/
https://streetscience.usegalaxy.eu/
https://usegalaxy.be/
https://usegalaxy.eu/
https://usegalaxy.fr/
https://usegalaxy.no/
https://usegalaxy.org/
https://usegalaxy.org.au/

pro: no installation required, usable directly
cons: some limitations and slow (or super slow) when running big computations

2) Use our local Galaxy server (IRCAN institute, in Pasteur tower)

http://galaxy-metag.ircan.org/

pro: no installation required, usable directly
cons: should to be faster than previous servers, but depending the number of students connected at the same time !

3) Install Galaxy on your own computer

- install “docker” tool here
- install a Galaxy server into Docker and run docker, by typing this single command:

docker run -p 8080:80 quay.io/galaxy/metagenomics-training

Wait a loooong time before it starts : 5-10 Go to download the first time! ⇒ do it at home using a fast internet connection. Further starts are faster (re type the same command to enable the server).

- Go here in your browser : http://localhost:8080

pro: fast server, depending of you computer power. Reusable.
cons: harder (and long) to install. Take some disk space onto your hard drive.

then,

• Create a personal account into Galaxy (top-right menu)

• Start this tutorial : Here (alternative link)