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I assume you just got a fresh clean BCF account to our system. What follows is a step by step guide on how to set up your account to work through our jupyter hub/lab and one or multiple conda environments:

  1. ssh into our system
  2. you might have to set proxy information
    export http_proxy="" && export https_proxy="" && export ftp_proxy=""

    to be able to connect to the internet

    1. using default install prefix is fine
    2. allow conda to initialize your shell, which should be bash
  3. either log out and ssh into the system again OR reload environment via
    . ~/.profile

    to let the system know about the newly installed conda.

  4. install nb_conda_kernels
    1. create a new subdirectory
      mkdir -p $HOME/Git/Anaconda-Platform
    2. change into this new directory
      cd $HOME/Git/Anaconda-Platform
    3. clone the repository
      git clone
    4. change into the newly cloned directory
      cd nb_conda_kernels
    5. install necessary dependencies and make sure you do so for the system python version
      /usr/bin/pip install traitlets jupyter_client --user
    6. install nb_conda_kernels
      /usr/bin/python3 develop --user
  5. install Qiime2
    1. change into your home directory
  6. create a jupyter configuration file
    touch `jupyter --config-dir`

    with following content. Should you encounter issues, read up more details at Most likely, a subdirectory like .jupyter does not exist yet in your home dir.

      "CondaKernelSpecManager": {
        "kernelspec_path": "--user"
  7. in your base environment execute
    /usr/bin/python3 -m nb_conda_kernels list
public/jlab/jupyter.txt · Last modified: 2021/10/06 13:19 by sjanssen