We are assuming you have a working
mamba installation in your computer.
If this is not the case, please refer to their official documentation.
If you installed
mamba into an existing
conda installation, also make sure that the
conda-forge channel is configured by running
conda config --add channels conda-forge.
If you prefer to work with
conda, please use
conda in place of
mamba in the instructions below.
Please note that the TeachOpenCADD setup with
conda takes much longer than with
Install from the conda package¶
The conda package does not yet include all packages necessary to run the deep learning edition talktorials (T033-T038).
We are working on it and will post an update as soon as the new package is available.
Create a new conda environment for TeachOpenCADD:
# Linux / MacOS mamba create -n teachopencadd teachopencadd # Windows mamba create -n teachopencadd teachopencadd -c conda-forge -c defaults # When using a MacBook Air 12.4 with an M1 chip you may need: CONDA_SUBDIR=osx-64 mamba create -n teachopencadd teachopencadd
Activate the new environment:
conda activate teachopencadd
teachopencadd -hto test that it works.
teachopencadd start .to set up a new workspace with the TeachOpenCADD material. Follow the instructions printed in your terminal to open the material (Jupyter notebooks) with Jupyter Lab. In this example command, you are setting up your workspace in the current directory
.; you can use any other path.
You can always return to your TeachOpenCADD material with
jupyter lab /path/to/your/teachopencadd/workspace.
If you need an introduction to Jupyter notebooks, please check out the suggested resources here.
Install from the latest development snapshot¶
Create a new conda environment and activate it:
mamba env create -f https://raw.githubusercontent.com/volkamerlab/TeachOpenCADD/master/devtools/test_env.yml conda activate teachopencadd
Note: If you are working on MacOS with an M1 chip and the above command is not working, e.g. “The environment can’t be solved, aborting the operation”, prefix the command with
CONDA_SUBDIR=osx-64and try again:
CONDA_SUBDIR=osx-64 mamba env create -f https://raw.githubusercontent.com/volkamerlab/TeachOpenCADD/master/devtools/test_env.yml conda activate teachopencadd
Download a zipfile of the repository using this link.
Unzip to your location of choice.
Navigate to your location.
Start Jupyter Lab.
Double click on the lesson you want to start.
Steps 2 to 5 are summarized below.
Instructions for Linux / MacOS
wget https://github.com/volkamerlab/teachopencadd/archive/master.zip -O teachopencadd.zip mkdir -p ~/Documents unzip teachopencadd.zip -d ~/Documents cd ~/Documents/teachopencadd-master/teachopencadd/talktorials jupyter lab
Instructions for Windows (PowerShell)
wget https://github.com/volkamerlab/teachopencadd/archive/master.zip -O teachopencadd.zip mkdir ~/Documents/ Expand-Archive teachopencadd.zip -d ~/Documents cd ~/Documents/teachopencadd-master/teachopencadd/talktorials jupyter lab