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Enable Jupyter kernels for batch execution #61

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Merged
bgruening merged 11 commits into from
Apr 18, 2025
Merged

Enable Jupyter kernels for batch execution #61

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607a139
Enable Jupyter kernels for batch execution
TuturBaba Mar 25, 2025
5cc002f
Update Dockerfile
TuturBaba Mar 26, 2025
12cf0e4
Update Dockerfile
TuturBaba Mar 26, 2025
91f75f3
Update Dockerfile
TuturBaba Mar 26, 2025
25607a5
Update Dockerfile
TuturBaba Mar 26, 2025
99d8cfb
Update Dockerfile
TuturBaba Mar 26, 2025
6e5b978
Update Dockerfile
TuturBaba Mar 26, 2025
0adf41e
Update Dockerfile
TuturBaba Mar 26, 2025
ad2c8d9
Configuration to .Rprofile
TuturBaba Apr 2, 2025
432d2bb
Improve kernel installation method and remove nb_conda_kernels
TuturBaba Apr 8, 2025
ef651ad
ADD PATH in .Rprofile
TuturBaba Apr 9, 2025
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54 changes: 31 additions & 23 deletions Dockerfile
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Expand Up @@ -35,33 +35,41 @@ RUN conda install --yes \
##
## Now create separate environments, that are managed by nb_conda_kernels
##
conda create -n ansible-kernel --yes ansible-kernel bioblend galaxy-ie-helpers && \
conda create -n bash-kernel --yes bash_kernel bioblend galaxy-ie-helpers && \
conda create -n octave-kernel --yes octave_kernel bioblend galaxy-ie-helpers && \
conda create -n python-kernel-3.12 --yes python=3.12 ipykernel bioblend galaxy-ie-helpers && \
conda create -n python-kernel-3.12 --yes python=3.12 ipykernel bioblend galaxy-ie-helpers && \
conda run -n python-kernel-3.12 python -m ipykernel install --user --name python-kernel-3.12 --display-name "Python 3.12" && \
conda create -n rlang-kernel --yes r-base r-irkernel r-xml rpy2 bioblend galaxy-ie-helpers \
'r-caret' \
'r-crayon' \
'r-devtools' \
'r-e1071' \
'r-forecast' \
'r-hexbin' \
'r-htmltools' \
'r-htmlwidgets' \
'r-irkernel' \
'r-nycflights13' \
'r-randomforest' \
'r-rcurl' \
'r-rmarkdown' \
'r-rodbc' \
'r-rsqlite' \
'r-shiny' \
'r-tidymodels' \
'r-tidyverse' \
'unixodbc' && \
'r-caret' \
'r-crayon' \
'r-devtools' \
'r-e1071' \
'r-forecast' \
'r-hexbin' \
'r-htmltools' \
'r-htmlwidgets' \
'r-irkernel' \
'r-nycflights13' \
'r-randomforest' \
'r-rcurl' \
'r-rmarkdown' \
'r-rodbc' \
'r-rsqlite' \
'r-shiny' \
'r-tidymodels' \
'r-tidyverse' \
'unixodbc' && \
conda run -n rlang-kernel R -e 'IRkernel::installspec(user = TRUE)' && \
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@bgruening bgruening Mar 29, 2025

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You can also add here something like (name = 'rlang-kernel', displayname = 'R')

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@bgruening bgruening Mar 29, 2025

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and I guess for the other kernels as well

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@TuturBaba TuturBaba Apr 2, 2025

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Yes u can : conda run -n rlang-kernel R -e "IRkernel::installspec(user = TRUE, name = 'rlang-kernel', displayname = 'R')"
But it's also possible without specifying a name: conda run -n python-kernel-3.12 python -m ipykernel install --user

conda create -n bash-kernel --yes bash_kernel bioblend galaxy-ie-helpers && \
conda run -n bash-kernel python -m bash_kernel.install --user && \
conda create -n octave-kernel python=3.8 --yes && \
conda run -n octave-kernel pip install octave_kernel bioblend galaxy-ie-helpers && \
conda run -n octave-kernel python -m octave_kernel install --user&& \
conda create -n ansible-kernel --yes ansible-kernel jupyter_client bioblend galaxy-ie-helpers && \
conda run -n ansible-kernel python -m ansible_kernel.install && \
conda clean --all -y && \
chmod a+w+r /opt/conda/ -R



ADD ./startup.sh /startup.sh
#ADD ./monitor_traffic.sh /monitor_traffic.sh
ADD ./get_notebook.py /get_notebook.py
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