Install and Run BioExcel Building Blocks in Mac OS Apple Silicon

Install Miniconda

1. Go to the official Miniconda website:
   
   https://docs.conda.io/projects/miniconda/en/latest/
2. Download the Intel x86 bash. At the moment of writting this tutorial, that was the best choice because most of the dependencies had not specific ARM version yet. Using the Intel version will ensure finding all the dependencies. .
   
   
3. Open a Terminal in the folder where the downloaded file is and type the following instruction:
   
   

   $ bash Miniconda3-latest-MacOSX-x86_64.sh

4. After finishing the installation, be sure that everything worked typing:
   
   

   $ conda info

   The output should be something like:
   
   

       active environment : None
              shell level : 0
         user config file : /path/to/.condarc
   populated config files : /path/to/.condarc
            conda version : 23.5.2
      conda-build version : not installed
           python version : 3.11.4.final.0
         virtual packages : __archspec=1=x86_64
                            __osx=10.16=0
                            __unix=0=0
         base environment : /path/to/miniconda3  (writable)
        conda av data dir : /path/to/miniconda3/etc/conda
    conda av metadata url : None
             channel URLs : https://repo.anaconda.com/pkgs/main/osx-64
                            https://repo.anaconda.com/pkgs/main/noarch
                            https://repo.anaconda.com/pkgs/r/osx-64
                            https://repo.anaconda.com/pkgs/r/noarch
            package cache : /path/to/miniconda3/pkgs
                            /path/to/.conda/pkgs
         envs directories : /path/to/miniconda3/envs
                            /path/to/.conda/envs
                 platform : osx-64
               user-agent : conda/23.5.2 requests/2.29.0 CPython/3.11.4 Darwin/21.5.0 OSX/10.16 solver/libmamba conda-libmamba-solver/23.5.0 libmambapy/1.4.1
                  UID:GID : XXXXXXXXXX:XXXXXXXXXX
               netrc file : None
             offline mode : False

5. Additionally, it's highly recommended to enable libmamba as solver for the sake of improving the time when solving complex environments:
   
   

   $ conda config --set solver libmamba

   This package comes usually preinstalled, but if it's not present, then execute the next instruction in the base environment:
   
   

   $ conda install -n base conda-libmamba-solver

   For reverting to the classic solver, type:
   
   

   conda config --set solver classic

Install Git

If you have Git installed (to test it, just type git in your terminal), please skip this step. If not, go to the next link and install it:

https://git-scm.com/download/mac

Run tutorial

Go to the tutorial and follow the instructions. As an exemple we have taken the Protein MD Setup tutorial:

https://github.com/bioexcel/biobb_wf_md_setup

Then, please follow the next steps:

1. First off, download the tutorial cloning the project in your computer:
   
   

   git clone https://github.com/bioexcel/biobb_wf_md_setup.git

2. Go to the project folder:
   
   

   cd biobb_wf_md_setup

3. Create anaconda environment:
   
   

   conda env create -f conda_env/environment.yml

4. The creation of the environment will take some minutes. Once it's done, let's activate the environment:
   
   

   conda activate biobb_MDsetup_tutorial

   In some distributions, conda activate instruction doesn't work. If this is the case, please type:
   
   

   source activate biobb_MDsetup_tutorial 

5. Activate Jupyter extensions:
   
   

   jupyter-nbextension enable --py --user widgetsnbextension
   jupyter-nbextension enable --py --user nglview

6. Open Jupyter Notebook:
   
   

   jupyter-notebook biobb_wf_md_setup/notebooks/biobb_MDsetup_tutorial.ipynb

7. Jupyter Notebook is a web-based interactive computational environment. When launching the above instruction the default browser is automatically launched. If this is not the case, copy all the address provided by Jupyter Notebook (with the long token included) and copy it to your browser:
   
   

   [I 17:10:51.920 NotebookApp] Serving notebooks from local directory: /home/USER/projects/BioBB/tutorials
   [I 17:10:51.920 NotebookApp] The Jupyter Notebook is running at:
   [I 17:10:51.920 NotebookApp] http://localhost:8888/?token=71e022a6ac0f6e31efb37f4d12053a36bbfe7f22f0625266
   [I 17:10:51.920 NotebookApp] Use Control-C to stop this server and shut down all kernels (twice to skip confirmation).
   [C 17:10:51.925 NotebookApp] 
       
       To access the notebook, open this file in a browser:
           file:///home/USER/.local/share/jupyter/runtime/nbserver-29420-open.html
       Or copy and paste one of these URLs:
           http://localhost:8888/?token=71e022a6ac0f6e31efb37f4d12053a36bbfe7f22f0625266
   Opening in existing browser session.

8. This tutorial has been successfully tested in Safari, Google Chrome and Mozilla Firefox.