python with conda

A very short guide for installing python packages (pymol in this example) as a non-privileged user, inside a (python) virtual environment created with conda (miniconda).

1. Set conda installation home (CHOME) in bash:
   export CHOME=/home/myhome

2. Download (mini)conda with wget (always download the latest version if you want to use python latest version):
   wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh

3. Install miniconda in $CHOME/miniconda:
   bash miniconda.sh -b -p $CHOME/miniconda

4. Set path for executing conda (needed once):
   export PATH="$CHOME/miniconda/bin:$PATH"

5. Create a virtual environment named "pymol" with python 3.9 and numpy
   (python version in virtual environment may differ from system-wide)
   conda create -n pymol python=3.9 numpy -y

6. Set conda enviroment variables (needed every time you use virtual environment):
   . $CHOME/miniconda/etc/profile.d/conda.sh

7. Activate "pymol" virtual environment, i.e. work with python and packages in "pymol" virtual environment, not those system-wide:
   conda activate pymol

8. Install (see 9. for open-source package) licensed pymol package from conda/schroedinger repos (30 days trial or a license is needed):
   conda install -c conda-forge -c schrodinger pymol-bundle

9. Install (see 8. for licensed package) open-source pymol package from conda repos:
   conda install -c conda-forge pymol-open-source

10. Deactivate "pymol" virtual enviroment (or exit shell), i.e. clean up current shell, if needed:
    conda deactivate

11. Run pymol in a new shell:
    . $CHOME/miniconda/etc/profile.d/conda.sh
    conda activate pymol
    pymol