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#! /bin/sh -e
# genenetwork-machines --- Guix configuration for genenetwork machines
# Copyright © 2025 Munyoki Kilyungi <me@bonfacemunyoki.com>
#
# 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/>.
# Build and install genenetwork container on your local machine.
set -euo pipefail
BASE_DIR="${HOME:-/home/$USER}/genenetwork"
SYSTEM_DIRECTORIES=(
"$BASE_DIR/var/log"
"$BASE_DIR/var/genenetwork"
"$BASE_DIR/etc/genenetwork/conf"
"$BASE_DIR/etc/genenetwork"
"$BASE_DIR/var/lib/redis"
"$BASE_DIR/var/lib/virtuoso"
"$BASE_DIR/var/lib/xapian"
"$BASE_DIR/var/lib/genenetwork-sqlite"
"$BASE_DIR/var/lib/genenetwork-gnqa"
"/tmp/local-container"
)
GN_PROJECTS=(
"genenetwork2:git@github.com:genenetwork/genenetwork2"
"genenetwork3:git@github.com:genenetwork/genenetwork3"
"gn-auth:https://git.genenetwork.org/gn-auth"
"gn-docs:https://git.genenetwork.org/gn-docs"
)
CONTAINER_SCM="genenetwork-local-container.scm"
CONTAINER_BIN="/usr/local/bin/genenetwork-local-container"
GC_ROOT="/var/guix/gcroots/genenetwork-local-container"
log() {
local level="$1"
shift
echo "[$(date '+%Y-%m-%d %H:%M:%S')] $level: $*" >&2
}
# Check dependencies
for cmd in git guix sudo; do
if ! command -v "$cmd" &>/dev/null; then
log "ERROR" "Required command '$cmd' not found"
exit 1
fi
done
# Validate HOME is set
if [ -z "${HOME:-}" ]; then
log "ERROR" "HOME environment variable is not set"
exit 1
fi
log "INFO" "Creating system directories..."
for dir in "${SYSTEM_DIRECTORIES[@]}"; do
# Check if directory exists and is accessible
if [ -d "$dir" ]; then
if [ -w "$dir" ]; then
log "DEBUG" "Directory exists and is writable: $dir"
else
log "WARNING" "Directory exists but is not writable: $dir"
fi
continue
fi
# Attempt to create directory
log "INFO" "Creating directory: $dir"
if [ -w "$(dirname "$dir")" ]; then
# Parent directory is writable, try without sudo
if ! mkdir -p "$dir"; then
log "ERROR" "Failed to create directory without sudo: $dir"
exit 1
fi
else
# Parent directory requires root, use sudo
if ! sudo mkdir -p "$dir"; then
log "ERROR" "Failed to create directory with sudo: $dir"
exit 1
fi
# Set ownership to current user if created with sudo
if ! sudo chown "$USER:$USER" "$dir"; then
log "WARNING" "Failed to set ownership for: $dir"
fi
fi
done
is_git_repository() {
local dir="$1"
# Check for standard repository
if [ -d "$dir/.git" ]; then
if [ -f "$dir/.git/HEAD" ] && [ -d "$dir/.git/refs" ]; then
log "DEBUG" "Detected standard Git repository: $dir"
return 0
else
log "ERROR" "Directory $dir/.git exists but is not a valid Git repository"
return 1
fi
# Check for bare repository
elif [ -f "$dir/HEAD" ] && [ -d "$dir/refs" ] && [ -d "$dir/objects" ]; then
log "DEBUG" "Detected bare Git repository: $dir"
return 0
else
log "ERROR" "$dir exists but is not a Git repository (neither standard nor bare)"
return 1
fi
}
# Clone GeneNetwork projects
log "INFO" "Cloning GeneNetwork projects..."
for project_entry in "${GN_PROJECTS[@]}"; do
IFS=':' read -r project repo_url <<< "$project_entry"
dir="$BASE_DIR/$project"
if [ ! -d "$dir" ]; then
log "INFO" "Cloning $project from $repo_url to $dir"
if ! git clone "$repo_url" "$dir"; then
log "ERROR" "Failed to clone $project"
exit 1
fi
else
log "DEBUG" "Directory exists, skipping clone: $dir"
if ! is_git_repository "$dir"; then
log "ERROR" "$dir exists but is not a Git repository"
exit 1
fi
fi
done
# Verify container SCM file exists
if [ ! -f "$CONTAINER_SCM" ]; then
log "ERROR" "Container SCM file not found: $CONTAINER_SCM"
exit 1
fi
# Create Guix system container
log "INFO" "Creating Guix system container..."
SHARE_OPTS=(
"--share=$BASE_DIR/var/log=/var/log"
"--share=$BASE_DIR/var/genenetwork=/var/genenetwork"
"--share=$BASE_DIR/etc/genenetwork/conf=/etc/genenetwork/conf"
"--share=$BASE_DIR/etc/genenetwork=/etc/genenetwork"
"--share=$BASE_DIR/var/lib/redis=/var/lib/redis"
"--share=$BASE_DIR/var/lib/virtuoso=/var/lib/virtuoso"
"--share=$BASE_DIR/genenetwork2=/genenetwork2"
"--share=$BASE_DIR/genenetwork3=/genenetwork3"
"--share=$BASE_DIR/gn-auth=/gn-auth"
"--share=$BASE_DIR/var/lib/xapian=/var/lib/xapian"
"--share=$BASE_DIR/var/lib/genenetwork-sqlite=/var/lib/genenetwork-sqlite"
"--share=$BASE_DIR/var/lib/genenetwork-gnqa=/var/lib/genenetwork-gnqa"
"--share=/tmp/local-container=/tmp"
"--share=$BASE_DIR/gn-docs=/var/lib/gn-docs"
"--share=/run/mysqld=/run/mysqld"
)
container_script=$(guix system container \
--network \
--load-path=. \
--verbosity=3 \
"${SHARE_OPTS[@]}" \
"$CONTAINER_SCM")
log $container_script
# Create symbolic links
log "INFO" "Creating symbolic links..."
if ! sudo ln -sf "$container_script" "$CONTAINER_BIN"; then
log "ERROR" "Failed to create symbolic link: $CONTAINER_BIN"
exit 1
fi
if ! sudo ln -sf "$container_script" "$GC_ROOT"; then
log "ERROR" "Failed to create GC root link: $GC_ROOT"
exit 1
fi
log "INFO" "Setup completed successfully!"
log "INFO" "Container script: $container_script"
log "INFO" "Run with: $CONTAINER_BIN"
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