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install datalad on the cluster

Installing Datalad on the CECI cluster for your user#

To contribute see here

  • First of all access one the clusters (this has been tried on Lemaitre4)
  • Upgrade pip.
# upgrade pip
pip3 install --user --upgrade pip
  • Following the guide from datalad handbook installation for HPC (no root access) or copy-paster the code below.
# get anaconda
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh

# install it
bash Miniconda3-latest-Linux-x86_64.sh

Check that conda is installed with conda --version and try again.

If this outputs that conda is command not found, try:

source .bashrc

Install datalad

conda install -c conda-forge datalad
  • Now let's try to clone from gin a repo on the cluster space using datalad:
# clone using the ssh path from a gin repo
datalad install git@gin.g-node.org:/USERNAME/REPONAME.git

# get the data
cd YOUR-CLONED-REPO
datalad get .

it won't probably work since ssh keys to github/gin/etc has to be set up.

Set up the einviroment as you did on your personal computer and remebere that if your password is not working is is possible that github/gin/etc are expecting the token code you have to create for each machine.

Some usefule links and notes (but not very tidy):

If you need to create an ssh key follow this on github website

or just type:

ssh-keygen -t ed25519 -C "your_email@example.com"

# print the ssh key to copy
cat ~/.ssh/id_ed25519.pub

and add it in your gin settings, "ssh key" section.