Update CGI computers remotely

Updates Ubuntu 14.04 computers with latest version of R, RStudio, R libraries, Python and BioPython, for bioinformatics training.

Remote computer requirements:

ClusterShell
ssh key authentication for all 10 laptops
Wired connection (wireless in the building is flaky)

Usage

Setup your /etc/hosts and map the target laptops as e.g. cgi01, cgi02, etc. The Ubuntu machines don't have openssh-server installed on them, so install it, copy the keys, and then disable password authentication.

# On the laptops
local$ sudo apt-get update && sudo apt-get -y install openssh-server
local$ sudo sed -i 's/#Pass.*/PasswordAuthentication no/' /etc/ssh/sshd_config

Then create an ssh keys and copy it over:

remote$ idf=~/.ssh/id_rsa-cgi-202
remote$ ssh-keygen -f $idf -N ""
remote$ for host in cgi{01..10}; do ssh-copy-id -i $idf cgi_user@$host; done

Add the identity file to your ~/.ssh/config

Host cgi*
     IdentityFile ~/.ssh/id_rsa-cgi-202
     User cgi_user

Test that the keys work with:

remote$ alias clush="clush -B -w cgi[01-10]"
remote$ type clush # verify alias
remote$ clush id -u
1000

On each computer, locally restart SSH server for the disabled password authentication to take effect.

local$ sudo service ssh restart

Running sudo remotely is a pain, so use the same key for remote root access.

local$ sudo mkdir -p /root/.ssh
local$ sudo sh -c "echo $(tail -1 ~/.ssh/authorized_keys) >> /root/.ssh/authorized_keys"
local$ sudo cat /root/.ssh/authorized_keys

In the present configuration, commands are normally executed as cgi_user. To execute as root, use the -l root option of clush:

remote$ clush -l root id -u
0
remote$ clush -l root --copy cgi-updater-payload.sh --dest /root/
remote$ clush -l root ls /root/
# Remove the `-B` flag to stream output to troubleshoot problems
remote$ alias clush="clush -w cgi[01-10]"
remote$ clush -l root ./cgi-updater-payload.sh

Finishing up

Verify R and biopython versions:

remote$ clush -B "R --version | awk 'NR == 1 {print \$3}'"
remote$ clush -B "pip show biopython | awk '/Version/ {print \$2}'"
remote$ clush -B dpkg-query --showformat='\${Version}' --show rstudio

coregenomics/cgi-updater

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