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#! /bin/bash -e
# This is a development machine used by Pjotr
#
# genenetwork-machines --- Guix configuration for genenetwork machines
# Copyright © 2022, 2024 Arun Isaac <arunisaac@systemreboot.net>
# Copyright © 2024 Pjotr Prins <pjotr.public01@thebird.nl>
#
# This file is part of genenetwork-machines.
#
# genenetwork-machines is free software: you can redistribute it
# and/or modify it under the terms of the GNU General Public License
# as published by the Free Software Foundation, either version 3 of
# the License, or (at your option) any later version.
#
# genenetwork-machines is distributed in the hope that it will be
# useful, but WITHOUT ANY WARRANTY; without even the implied warranty
# of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with genenetwork-machines. If not, see
# <https://www.gnu.org/licenses/>.
# See also https://issues.genenetwork.org/topics/systems/fire-up-genenetwork-system-container
# this script should not be run as root.
if [ "$EUID" -eq 0 ]
then echo "Please do not run as root."
exit
fi
echo Build and install genenetwork gndev container on $HOSTNAME
rm -rf /export2/guix-containers/gndev/tmp # muck out for testing
mkdir -p /export2/guix-containers/gndev/tmp
touch /export2/guix-containers/gndev/tmp/gndev-tmp
mkdir -p /export2/guix-containers/gndev/var/lib/acme
mkdir -p /export2/guix-containers/genenetwork/etc/genenetwork
mkdir -p /export2/data/gndev-xapian
mkdir -p /export2/data/gndev-sqlite
mkdir -p /export/data/gndev/genotype_files
# Note that if you change these paths you need to rebuild the container
container_script=$(~/opt/guix-gndev/bin/guix system container \
--network \
--load-path=.. -L ~/guix-bioinformatics \
--verbosity=3 \
--share=/export2/guix-containers/gndev/var/lib/acme=/var/lib/acme \
--share=/export2/guix-containers/gndev/tmp=/var/tmp \
--share=/export2/guix-containers/genenetwork/etc/genenetwork=/etc/genenetwork \
--share=/export2/data/gndev-xapian \
--share=/export2/data/gndev-sqlite \
--expose=/export/data/genenetwork/genotype_files \
--expose=/export/data/gndev \
--share=/var/run/mysqld=/run/mysqld \
--share=/export/source/gndev-debug \
gndev.scm)
name=/usr/local/bin/gndev-system-container
if [ $? == 0 ] ; then
echo "Create $name -> $container_script"
sudo ln --force --symbolic $container_script $name
sudo ln --force --symbolic /usr/local/bin/$name /var/guix/gcroots
fi
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