BCF Wiki

This page is read only. You can view the source, but not change it. Ask your administrator if you think this is wrong.
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:
  - ssh into our system
  - you might have to set proxy information <code>export http_proxy="http://proxy.computational.bio.uni-giessen.de:3128" && export https_proxy="http://proxy.computational.bio.uni-giessen.de:3128" && export ftp_proxy="http://proxy.computational.bio.uni-giessen.de:3128"</code> to be able to connect to the internet
  - install Miniconda3: [[https://docs.conda.io/en/latest/miniconda.html]]
    - using default install prefix is fine
    - allow conda to **init**ialize your shell, which should be bash
  - either log out and ssh into the system again OR reload environment via <code>. ~/.profile</code> to let the system know about the newly installed conda.
  - install ''nb_conda_kernels''
    - create a new subdirectory <code>mkdir -p $HOME/Git/Anaconda-Platform</code>
    - change into this new directory <code>cd $HOME/Git/Anaconda-Platform</code>
    - clone the repository <code>git clone https://github.com/Anaconda-Platform/nb_conda_kernels.git</code>
    - change into the newly cloned directory <code>cd nb_conda_kernels</code>
    - install necessary dependencies and make sure you do so for the system python version <code>/usr/bin/pip install traitlets jupyter_client --user</code>
    - install ''nb_conda_kernels'' <code>/usr/bin/python3 setup.py develop --user</code>
  - install Qiime2
    - change into your home directory<code>cd</code>
    - follow [[https://docs.qiime2.org/2021.8/install/native/#install-qiime-2-within-a-conda-environment]]
  - install "ggmap": [[https://github.com/sjanssen2/ggmap]]
  - create a jupyter configuration file <code>touch `jupyter --config-dir`</code> with following content. Should you encounter issues, read up more details at [[https://github.com/Anaconda-Platform/nb_conda_kernels]]. Most likely, a subdirectory like ''.jupyter'' does not exist yet in your home dir.<code>
{
  "CondaKernelSpecManager": {
    "kernelspec_path": "--user"
  }
}
</code>
  - in your base environment execute <code>/usr/bin/python3 -m nb_conda_kernels list</code>
  - you should be done! Log in to [[https://www.computational.bio.uni-giessen.de/jupyter/]]