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RW-12661 Support qiime #4831

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RW-12661 Support qiime #4831

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support qiime
Qi77Qi Mar 10, 2025
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Qi77Qi Mar 10, 2025
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chown
Qi77Qi Mar 12, 2025
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Qi77Qi Mar 12, 2025
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Qi77Qi Mar 12, 2025
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Qi77Qi Mar 13, 2025
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Qi77Qi Mar 17, 2025
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11 changes: 11 additions & 0 deletions http/src/main/resources/init-resources/gce-init.sh
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Expand Up @@ -564,6 +564,17 @@ if [ ! -z "$JUPYTER_DOCKER_IMAGE" ] ; then
# This is to make it so that older images will still work after we change notebooks location to home dir
docker exec ${JUPYTER_SERVER_NAME} sed -i '/^# to mount there as it effectively deletes existing files on the image/,+5d' ${JUPYTER_HOME}/jupyter_notebook_config.py

# custom code only for AoU image. We can remove this after AoU maintenance mode is over in 2026.
if [[ $JUPYTER_DOCKER_IMAGE == *terra-jupyter-aou* ]]; then
# retry 3 docker exec ${JUPYTER_SERVER_NAME} pip install --upgrade jupyter-server
# retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} sudo -E -u jupyter jupyter serverextension enable --py qiime2
# retry 3 docker exec -u root -e PIP_USER=false ${JUPYTER_SERVER_NAME} chown -R jupyter:users $JUPYTER_USER_HOME/.config
retry 3 docker exec -u root ${JUPYTER_SERVER_NAME} chown -R jupyter:users $JUPYTER_USER_HOME/
retry 3 docker exec ${JUPYTER_SERVER_NAME} /opt/conda/envs/qiime2-2024.10/bin/pip install --upgrade jupyter-server
retry 3 docker exec -u root ${JUPYTER_SERVER_NAME} chown -R jupyter:users /opt/conda/envs/qiime2-2024.10/etc
retry 3 docker exec ${JUPYTER_SERVER_NAME} /opt/conda/envs/qiime2-2024.10/bin/jupyter server extension enable --py qiime2 --sys-prefix
fi

log 'Starting Jupyter Notebook...'
retry 3 docker exec -d $JUPYTER_SERVER_NAME /bin/bash -c "${JUPYTER_SCRIPTS}/run-jupyter.sh ${NOTEBOOKS_DIR}"

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