/mt

master thesis project

Primary LanguageJupyter Notebook

MT

Installation on Merlin

Create a conda env:

module load anaconda
conda env create -f environment.yml --prefix=/data/project/bio/schertler/Flurin/mtenv

Activate (command line)

conda activate /data/project/bio/schertler/Flurin/mtenv

To just the environment to show up in jupyter, you may need to run (within the environment)

python -m ipykernel install --user --name mtenv --display-name "Python [conda env:mtenv]"

Jupyterhub (Merlin)

  1. Clone the repo

    git clone git@github.com:flurinh/mt.git

  2. Install the env into jupyter. (needs testing)

    conda activate /data/project/bio/schertler/Flurin/mtenv python -m ipykernel install --user --name mtenv --display-name "Python [conda env:mtenv]"

I'm not sure whether this is necessary or sufficient to make the environemnt show up in jupyterhub. See merlin-jupyter docs

  1. Launch jupyterhub: https://merlin-jupyter.psi.ch:8000

  2. Nagivate to your clone and open WALKTHROUGH.ipynb

  3. Go to Kernel > Change kernel > Python [conda env:mtenv]

  4. Go to Cell > Run all

Adding dependencies

New dendencies should be added to environment.yml. After adding something, update:

conda env update -f environment.yml