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]"
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Clone the repo
git clone git@github.com:flurinh/mt.git
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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
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Launch jupyterhub: https://merlin-jupyter.psi.ch:8000
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Nagivate to your clone and open
WALKTHROUGH.ipynb
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Go to Kernel > Change kernel > Python [conda env:mtenv]
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Go to Cell > Run all
New dendencies should be added to environment.yml. After adding something, update:
conda env update -f environment.yml