Installation of Galaxy & (many) dependencies on Ubuntu / Biolinux

galaxy-ubuntu-biolinux

# Follow steps 1-4 on Ubuntu or 2-4 on Biolinux

1. Add repositories to your machine configuration

a. Bio-Linux
$ sudo add-apt-repository “deb http://nebc.nerc.ac.uk/bio-linux/ unstable bio-linux”
$ sudo apt-get update
$ sudo apt-get install bio-linux-keyring

b. CRAN
Switch to using the CRAN version of R for Ubuntu. Bio-Linux uses an up-to-date version of R from the CRAN repository whereas default Ubuntu uses an older version of R. We are currently testing on the CRAN version and are not sure whether the final Galaxy packaging will require the CRAN version or not.

$ sudo add-apt-repository "deb http://www.stats.bris.ac.uk/R/bin/linux/ubuntu lucid/"
$ sudo add-apt-repository "deb-src http://www.stats.bris.ac.uk/R/bin/linux/ubuntu lucid/"
$ gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
$ gpg -a --export E084DAB9 | sudo apt-key add -
$ sudo apt-get update
$ sudo apt-get upgrade

2. Install UCSC packages

Download ucsc-tools-non-free:
$ wget http://nebc.nerc.ac.uk/downloads/bio-linux/ucsc-tools-non-free_3.1-2_amd64.deb
$ sudo dpkg -i ucsc-tools-non-free_3.1-2_amd64.deb

3. Install and run Galaxy with all the dependencies

Open a terminal and type the following commands
$ sudo apt-get update
$ sudo apt-get install galaxy-server-all

4. Open galaxy web interface

Go to: Applications ⇒ Bioinformatics ⇒ Galaxy