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Galen new user setup

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Jochen Weile edited this page Apr 4, 2024 · 3 revisions

Galen new user setup

After our move to the University of Pittsburgh, we have been granted a grace period on galen until approximately September 2024, after which we will no longer have access to this resource.

Learning how to use the Unix command line

Follow the Unix 101 tutorials here:

Setting up your environment

Set up modules

Disable the gnu12 module and save this module state. Otherwise this will interfere with the default R installation.

module reset
module unload gnu12
module save

Modify your .bashrc to automatically restore this saved state every time you log-in. While we're in here, we can also add a python alias and a new path entry and also increase the number of files allowed to be opened simultaneously for bcl2fastq to work. Before we make any changes, let's make a backup copy just in case:

cp ~/.bashrc ~/.bashrc.backup

To edit the file, use nano (or if you know what you're doing, use vim or any editor of your choice).

nano ~/.bashrc

Then add the following lines to the end of the file:

case "$HOSTNAME" in
    #load custom default module state (with gnu9 module disabled)
    galen*) module restore;;
    #increase number of file handles allowed for bcl2fastq
    rothseq1*) ulimit -n 2048;;
esac

#create a python alias
alias python='python3.8'
#add the .local/bin folder to your PATH variable
export PATH=$HOME/.local/bin:$PATH

If you used nano, save with CTRL-S and exit with CTRL-X.

If .local/bin (and bin/) don't exist yet, make sure to create them now.

mkdir -p ~/.local/bin/ ~/bin/

Install clusterutil

#create a downloads folder
mkdir downloads
cd downloads
#clone the clusterutil repo
git clone https://github.com/jweile/clusterUtil.git
#change to repo folder
cd clusterUtil
#run installer
bash install.sh

Install miniconda

#go back to the downloads folder
cd ~/downloads/
#download conda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
#install conda
bash Miniconda3-latest-Linux-x86_64.sh
  • Follow the on-screen prompts
  • Now, log out (via exit) and in again (via ssh) to update the session

Install python version 3.8

Even though it's technically already installed, the accompaying libraries are not well maintained by the sysadmin. So we install our own copy:

conda install python=3.8
#follow prompts again
#update all packages afterwards
conda update --all

Setting up a github access token

Both at the LTRI and the Donnelly Centre a great number of people access Github on a daily basis all while sharing the same external IP address. From Github's perspective this can appear as a single IP address spamming it with access requests, thus throttling or temporarily banning access from our institutions. This is a problem when installing R packages directly from github, as this requires frequent access to it.

To get around those access limits, Github offers Personal Access Tokens (PATs), which looks like a string of random letters and numbers that serves as an application-specific password to your account. To learn how to create your PAT, refer to the relevant github help page.

Once you have generated a PAT, you can let R know to use it for future installations.

  1. Go to your home directory and create a file called .Renviron 
cd ~
nano .Renviron
  1. Type GITHUB_PAT= and then copy-paste your PAT string after the = sign. Finally, press Enter to add a new line at the end
  2. Save and exit nano (CTRL-S and CTRL-X)

Optional installations

Clone this wiki locally