setup.sh
#!/usr/bin/env bash
set -e
# GitHub Actions pinned an older mysql-client version on runners temporarily
# due to an issue with the new version, so installation is not currently possible,
# see https://github.com/actions/virtual-environments/pull/4674; uncomment once fixed
# sudo apt-get mysql-client
sudo apt-get install libffi-dev build-essential apg
# Use examplar configuration for the beginning
cd website
# create example database
SQL_PASS=$(apg -m 128 -n 1 -E "\"'")
mv example_database.sql database.sql
sed "s|user|test_user|" database.sql -i
sed "s|pass|$SQL_PASS|" database.sql -i
sed "s|localhost|%|" database.sql -i
cat database.sql
echo "MySQL user: $MYSQL_USER"
mysql --host 127.0.0.1 --port "$MYSQL_PORT" -u "$MYSQL_USER" -p"$MYSQL_PASSWORD" < database.sql
echo "Database created"
mysql --host 127.0.0.1 --port "$MYSQL_PORT" -u "$MYSQL_USER" -p"$MYSQL_PASSWORD" -e 'SHOW DATABASES;'
mv example_config.py config.py
sed "s|user:pass@localhost|test_user:$SQL_PASS@127.0.0.1:$MYSQL_PORT|" config.py -i
R_LIBS_SITE=$(Rscript -e 'cat(paste(.libPaths(), collapse=":"))')
echo "R_LIBS_SITE: $R_LIBS_SITE"
sed "s|^R_LIBRARY_PATH = .*|R_LIBRARY_PATH = '$R_LIBS_SITE'|" config.py -i
R_HOME=$(R RHOME)
echo "R_HOME: $R_HOME"
sed "s|^R_HOME = .*|R_HOME = '$R_HOME'|" config.py -i
RANDOM_KEY=$(apg -m 128 -n 1 -E "\"'")
sed "s|^SECRET_KEY = .*|SECRET_KEY = \"$RANDOM_KEY\"|" config.py -i
cat config.py
cd ..
#git clone https://github.com/juanmirocks/Levenshtein-MySQL-UDF
#cd Levenshtein-MySQL-UDF
#echo `mysql_config --include`
#gcc -o levenshtein.so -fPIC -shared levenshtein.c `mysql_config --include` `mysql_config --include`/server
#sudo cp levenshtein.so `mysql_config --plugindir`
# for MariaDB use:
# plugin_dir=$(sudo mysql -e 'select @@plugin_dir;' | grep -v '@')
# sudo cp levenshtein.so $plugin_dir
#cd ..
#rm -rf Levenshtein-MySQL-UDF
# install autoprefixer, clean-css and nunjucks
npm install --global
# fix nunjucks to add jinja-compat mode for precompile
cd node_modules/nunjucks
wget https://github.com/mozilla/nunjucks/pull/1319.patch
patch -p1 < 1319.patch
rm 1319.patch
cd -
# rabbitmq-server: broker for celery
# keeping it down there as it takes quite some time
sudo apt-get install rabbitmq-server
# generate keys (for testing only!)
mkdir -p celery
cd celery
ssh-keygen -t rsa -b 4096 -f worker.key -q -N '' -m PEM
yes '' | openssl req -new -key worker.key -out worker.csr
openssl x509 -req -days 1 -in worker.csr -signkey worker.key -out worker.crt
cd ..
# prepare space for logs
mkdir -p website/logs
touch website/logs/app.log
# create tables for all databases and files for hash-based (HDB) databases
mkdir -p website/databases
mkdir -p website/databases/dna_to_protein
mkdir -p website/databases/gene_to_isoform
cd website
./manage.py migrate
cd ..
# create celery user
sudo groupadd celery
sudo useradd -g celery celery
cp celeryd .autogen_celeryd
sed "s|^CELERY_BIN=.*|CELERY_BIN=\"$(which celery)\"|" .autogen_celeryd -i
sed "s|^CELERYD_CHDIR=.*|CELERYD_CHDIR=\"$(pwd)\/website\"|" .autogen_celeryd -i
echo "Please modify /etc/default/celeryd script to adjust absolute paths to celery executable and website dir"
cat .autogen_celeryd
sudo cp .autogen_celeryd /etc/default/celeryd
mkdir temp -p
cd temp
wget https://raw.githubusercontent.com/celery/celery/3.1/extra/generic-init.d/celeryd
sudo mv celeryd /etc/init.d/celeryd
sudo chmod 755 /etc/init.d/celeryd
sudo chown root:root /etc/init.d/celeryd
cd ..
rm -r temp
# set access rights for celery
sudo apt-get install acl
setfacl -m u:celery:rwx website
setfacl -m u:celery:rwx website/logs
setfacl -m u:celery:rwx website/logs/app.log
setfacl -R -m u:celery:rwx celery
setfacl -R -m u:celery:rwx website/databases
# redis
sudo apt-get install redis-server
# (re) start everything
sudo /etc/init.d/celeryd restart
sudo /etc/init.d/redis-server restart
# install ActiveDriver and progress bar
# R -e 'install.packages("ActiveDriver")'
# fetch forked copy of ActiveDriver
cd website
git clone https://github.com/krassowski/ActiveDriver
cd ..
# ActivePathways will hopefully be on cran soon
# git clone https://github.com/reimandlab/activeDriverPW.git
# R -e 'install.packages(c("metap", "data.table"), repos = "http://cran.us.r-project.org")'
# R -e 'install.packages("activeDriverPW", repos=NULL)'
git clone https://github.com/reimandlab/rmimp.git
cd rmimp
git checkout refactored
cd ..
export R_INSTALL_STAGED=false
Rscript -e 'install.packages("rmimp", repos=NULL)'
Rscript -e 'found = "rmimp" %in% rownames(installed.packages()); cat("rmimp installed: ", found, "\n"); quit(status=as.numeric(!found))'
# sudo apt-get install libcairo2-dev - needed for svglite
# needed only if using sqlite3 for tests
sudo apt-get install sqlite3 sqlite3-pcre
# pip3 install pygraphviz
# on ubuntu:
# pip3 install pygraphviz --install-option="--include-path=/usr/include/graphviz" --install-option="--library-path=/usr/lib/graphviz/"
# on debian
# sudo apt-get install libcgraph6 graphviz graphviz-dev