start-jupyter

#!/bin/bash

eval "$(conda shell.bash hook)"

echo "-----> Population Genomics Course"
if [ ! -d "/usr/Material/Data" ] 
then 
    echo "downloading data"
    mkdir -p /usr/Material/Data
    wget https://zenodo.org/record/7551294/files/Data.tar.gz?download=1 -O /usr/Material/Data.tar.gz
    tar -zxvf /usr/Material/Data.tar.gz -C /usr/Material/Data
    rm -f /usr/Material/Data.tar.gz 
fi

if [ ! -d "${CONDA_DIR}/envs/popgen_au_env" ] 
then 
    mkdir -p ${CONDA_DIR}/envs/popgen_au_env
    wget -t 10 -O ${CONDA_DIR}/envs/popgen.tar.gz https://zenodo.org/record/7551294/files/popgen_au_env.tar.gz?download=1;
    tar -zxvf ${CONDA_DIR}/envs/popgen.tar.gz -C ${CONDA_DIR}/envs/popgen_au_env
    rm -f ${CONDA_DIR}/envs/popgen.tar.gz
fi

#conda activate ${CONDA_DIR}/envs/popgen_au_env

echo "-----> Installing course kernels on jupyterlab"
${CONDA_DIR}/envs/popgen_au_env/bin/python -m ipykernel install --user --name="args_dashboard" --display-name "args dashboard" && \
${CONDA_DIR}/envs/popgen_au_env/bin/R -e "IRkernel::installspec(user=TRUE, name = 'popgen_course', displayname = 'popgen course')" && \
${CONDA_DIR}/envs/popgen_au_env/bin/python -m bash_kernel.install && \
fix-permissions "/home/${NB_USER}" && \
ln -s /usr/Material /home/${NB_USER}/work/Course_Material

cp /usr/uCloud/Configurations/kernelBash.json ~/.local/share/jupyter/kernels/bash/kernel.json && \
ln -sf ${CONDA_DIR}/envs/popgen_au_env/lib/libcrypto.so.3 ${CONDA_DIR}/envs/popgen_au_env/lib/libcrypto.so.1.0.0

#jupyter labextension install /usr/Splashscreen/

printf  "\n==================  "
printf  "\n Start JupyterLab  \n"
printf  "==================  \n\n"
#add course name as variable to be used
bash -c "COURSE=${COURSE} jupyter lab --NotebookApp.token='' "