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Conda on Bianca

We have mirrored all major non-proprietary Conda repositories (not main, anaconda and r) directly on UPPMAX, on both Rackham and Bianca. These are updated every third day.

Available Conda channels

  • bioconda
  • biocore
  • conda-forge
  • dranew
  • free
  • main
  • pro
  • qiime2
  • r
  • r2018.11
  • scilifelab-lts
  • nvidia
  • pytorch

Warning

  • Good to change CONDA_ENVS_PATH to project folder, because of many small files.
  • Example: CONDA_ENVS_PATH=/proj/sens2023598/bjornc/conda
Read Conda user guide

Exercises

Tip

  • You may want to have the same path for all conda environments in the present project
  • echo "export CONDA_ENVS_PATH=/a/path/to/a/place/in/your/project/" >> ~/.bashrc
    • Example: echo "export CONDA_ENVS_PATH=/proj/sens2023598/bjornc/conda" >> ~/.bashrc

Warning

  • It seems you are required to use this path, ending with the name of your environment, together with --prefix when you install new envronments AND packages also after activating the conda environment! Like: conda install --prefix $CONDA_ENVS_PATH/<your-environment> ...
Create a conda environment and install some packages

  • First check the current installed packages while having python/3.9.5 loaded

  • Open a new terminal and have the old one available for later comparison

  • Make sure python module is not active in the new terminal

  • Start conda module

  • Make sure you have a folder in the project directory ($USER will automatically fill in you username. Handy!!)

  • mkdir /proj/sens2023598/$USER

  • mkdir /proj/sens2023598/$USER/conda

  • Set a CONDA_ENVS_PATH

    • Example: echo "export CONDA_ENVS_PATH=/proj/sens2023598/$USER/conda" >> ~/.bashrc

  • Use the conda module on Bianca and the conda-forge channel to create an environment with name bianca-course with python 3.7 and numpy 1.15

  • Use your a path for CONDA_ENVS_PATH

    • It may take a couple of minutes or so and do not forget to press y when asked for!

  • Activate!

  • Check with pip list what is there. Compare with the environment given from the python module in the first terminal window.

  • Which version of Python did you get?

  • Don't forget to deactivate the Conda environment before doing other exercises!

Solution

Write this in the terminal

$ module load conda
($ export CONDA_ENVS_PATH=/proj/sens2023598/$USER)
$ conda create -c conda-forge --prefix $CONDA_ENVS_PATH/bianca-course python=3.7 numpy=1.15
$ source activate bianca-course
$ pip list
$ python -V
$ conda deactivate
  • It should show numpy=1.15 among others and the python version 3.7.X for the conda env

keypoints

  • Conda is an installer of packages but also bigger toolkits

  • Conda on Bianca is easy since the repos in the most used channels are local.

  • Conda creates isolated environments not clashing with other installations of python and other versions of packages

  • Conda environment requires that you install all packages needed by yourself, although automatically.

  • That is, you cannot load the python module and use the packages therein inside your Conda environment.