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Jupyter notebook teaching environment

Table of Contents

Introduction

Guix installation

~/opt/guix/bin/guix package -i jupyter python-pandas vim screen tree 4store -p /usr/local/guix-profiles/jupyter

LIST=”python-mysqlclient python-sql python-sqlalchemy python jupyter python-pandas vim screen tree \ 4store python-pyvcf mc python-ipython sqlite python-elasticsearch python-requests raptor2 python-rdflib”

env GUIX_PACKAGE_PATH=./guix-bioinformatics/ ~/opt/guix/bin/guix package -p /usr/local/guix-profiles/jupyter -i $LIST

Note: python-elasticsearch needs to match the installed server’s major number

. /usr/local/guix-profiles/jupyter/etc/profile

or

env -i /bin/bash --login --noprofile --norc
export GUIX_PROFILE=/usr/local/guix-profiles/jupyter
export PATH=$GUIX_PROFILE/bin:$PATH
export JUPYTER_PATH=${GUIX_PROFILE}/share/jupyter
export PYTHONPATH=${GUIX_PROFILE}/lib/python3.7/site-packages:/home/jupyter/.local/lib/python3.7/site-packages
export GI_TYPELIB_PATH=${GUIX_PROFILE}/lib/girepository-1.0${GI_TYPELIB_PATH:+:}$GI_TYPELIB_PATH
export XDG_DATA_DIRS={GUIX_PROFILE}/share${XDG_DATA_DIRS:+:}$XDG_DATA_DIRS
jupyter notebook --notebook-dir=/home/jupyter/jupyter --no-browser --ip=192.168.8.9

From outside:

ssh -L 8888:192.168.8.9:8888 -f -N pjotrp@server

and point your browser to http://localhost:8888/

Password: bioinformatics

firewall-cmd --zone=public --add-port=8888/tcp
firewall-cmd --reload
firewall-cmd --zone=public --query-port=8888/tcp

Backups

We are using borg for backups which can be run from /usr/local/guix-profiles/jupyter/bin/borg

env BORG_PASSPHRASE=bioinformatics /usr/local/guix-profiles/jupyter/bin/borg create /data/backup/course-jupyter::Course-$(date +%A-%Y%m%d-%H:%M:%S) /home/jupyter/

4store

<!–

mkdir var/log/4store . /usr/local/guix-profiles/jupyter/etc/profile

echo ‘[4s-boss] discovery = sole nodes = 127.0.0.1 [pythoncourse] port = 8000 ’ > 4store.conf

4s-boss ps auxw | grep 4s-bos[s]

4s-admin -c 4store.conf list-nodes 4s-admin -c 4store.conf list-stores

[pjotrp@pubrec-cls-01 ~]$ 4s-admin -c 4store.conf list-nodes node_number hostname port status ip_address 0 127.0.0.1 6733 ok 127.0.0.1 [pjotrp@pubrec-cls-01 ~]$ 4s-admin -c 4store.conf list-stores store_name store_status backend_status pythoncourse available 1/1 running

Test if boss is listening telnet localhost 6733

export dbname=pythoncourse pkill 4s-backend-setup pkill 4s-httpd pkill 4s-backend

4s-backend $dbname 4s-httpd -c 4store.conf -D $dbname curl http://127.0.0.1:8000 This is a 4store SPARQL server firewall-cmd –zone=public –add-port=8000/tcp firewall-cmd –reload

–!>