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Setting up Local Development Database

You need to set up a quick local database for development without polluting your environment.

Method 1 (Using Guix system containers)

Setting up mariadb in a Guix container is the preferred and easier method. But, you need root access to run the container. The genenetwork2 repo comes with a guix system container definition to run MariaDB and Redis. From the genenetwork2 repo, you can build and run the container using:

$ sudo $(./containers/db-container.sh)

You should now be able to connect to the database using

$ mysql --protocol tcp -u root

Create a database db_webqtl_s

MariaDB [mysql]> CREATE DATABASE db_webqtl_s;

Load the small database dump into the database. You may find the small database either on space or tux02 at /home/aruni/gn2.sql.lz

$ lzip -cd gn2.sql.lz | mysql --protocol tcp -u root db_webqtl_s

Since this is a develpoment server accessible only from localhost, it is ok to use the root user with no password. Configure your development instance of genenetwork2 with the following SQL_URI.


Method 2 (running a local container)

A local container runs as a normal user. It requires some juggling of dirs to load an existing database. Make sure to not run on the same dirs as another mariadb instance(!)

cd ~/tmp/mariadb
mkdir var
~/tmp/mariadb$ ~/opt/guix-pull/bin/guix shell -C -N coreutils sed mariadb --share=var=/var --share=/export2/tmp=/tmp

inside the container

mkdir -p /var/lib/data
mkdir -p /var/lib/mysql
mkdir /var/run

Initialize with


and run

export TMPDIR=/tmp
mysqld_safe --datadir='./database' --port=3307 --user=$USER --nowatch --socket=/var/run/mysqld/mysqld.sock

Now from outside the container you should be able to connect with

stromboli:~/tmp/mariadb$ mysql --socket=var/run/mysqld/mysqld.sock


Welcome to the MariaDB monitor.  Commands end with ; or \g.
Your MariaDB connection id is 3
Server version: 10.5.12-MariaDB MariaDB Server

Copyright (c) 2000, 2018, Oracle, MariaDB Corporation Ab and others.

Type 'help;' or '\h' for help. Type '\c' to clear the current input statement.

MariaDB [(none)]> show databases;
| Database           |
| information_schema |
| mysql              |
| performance_schema |
| test               |
4 rows in set (0.001 sec)

If you need to tweak the server configuration you can load the my.cnf file with the `--defaults-file=var/my.cnf` inside and outside the container.

Method 3 (Manual method without Guix)

/This is not recommended/

  • An assumption is made that the GeneNetwork2 profile is in ~/opt/gn_profiles/gn2_latest for the purposes of this documentation. Please replace as appropriate.
  • We install the database files under ~/genenetwork/mariadb. Change as appropriate.

Set up directories

mkdir -pv ~/genenetwork/mariadb/var/run
mkdir -pv ~/genenetwork/mariadb/var/lib/data
mkdir -pv ~/genenetwork/mariadb/var/lib/mysql

Set up default my.cnf

cat <<EOF > ~/genenetwork/mariadb/my.cnf


Install the database

~/opt/gn_profiles/gn2_latest/bin/mysql_install_db \

Running the daemon:

~/opt/gn_profiles/gn2_latest/bin/mysqld_safe \

Connect to daemon

~/opt/gn_profiles/gn2_latest/bin/mysql \

Set up password for user

MariaDB [(none)]> USE mysql;
MariaDB [mysql]> ALTER USER '<your-username>'@'localhost' IDENTIFIED BY '<the-new-password>';

Now logout and login again with

$ ~/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=~/genenetwork/mariadb/my.cnf --password mysql

enter the newly set password and voila, you are logged in and your user has the password set up.

Now, set up a new user, say webqtlout, and a default database they can connect to

MariaDB [mysql]> CREATE DATABASE webqtlout;
MariaDB [mysql]> CREATE USER 'webqtlout'@'localhost' IDENTIFIED BY '<some-password>';
MariaDB [mysql]> GRANT ALL PRIVILEGES ON webqtlout.* TO 'webqtlout'@'localhost';

Now logout, and log back in as the new webqtlout user:

~/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=~/genenetwork/mariadb/my.cnf \
    --user=webqtlout --host=localhost --password webqtlout

and enter the password you provided.

Setting up the Small Database

Download the database from

Say you downloaded the file in ~/Downloads, you can now add the database to your server.

First stop the server:

$ ps aux | grep mysqld # get the process ids
$ kill -s SIGTERM <pid-of-mysqld> <pid-of-mysqld_safe>

Now extract the database archive in the mysql data directory:

$ cd ~/genenetwork/mariadb/var/lib/data
$ p7zip -k -d ~/Downloads/db_webqtl_s.7z

Now restart the server:

~/opt/gn_profiles/gn2_latest/bin/mysqld_safe \

Then update the databases

$ ~/opt/gn_profiles/gn2_latest/bin/mysql_upgrade \
    --defaults-file=~/genenetwork/mariadb/my.cnf \
    --user=frederick --password --force

and login as the administrative user:

$ ~/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=~/genenetwork/mariadb/my.cnf \
    --user=$(whoami) --password

and grant the privileges to your normal user:

MariaDB [mysql]> GRANT ALL PRIVILEGES ON db_webqtl_s.* TO 'webqtlout'@'localhost';

now logout as the administrative user and log back in as the normal user

~/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=~/genenetwork/mariadb/my.cnf \
    --user=webqtlout --host=localhost --password db_webqtlout_s

MariaDB [db_webqtlout_s]> SELECT * FROM ProbeSetData LIMIT 20;

verify you see some data.

A Note on Connection to the Server

So far, we have been connecting to the server by specifying --defaults-file option, e.g.

~/opt/gn_profiles/gn2_latest/bin/mysql \
    --defaults-file=~/genenetwork/mariadb/my.cnf \
    --user=webqtlout --host=localhost --password db_webqtlout_s

which allows connection via the unix socket.

We could drop that specification and connect via the port with:

~/opt/gn_profiles/gn2_latest/bin/mysql \
    --user=webqtlout --host= --port=3307 --password db_webqtlout_s

In this version, the host specification was changed from




whereas, the **--defaults-file** file specification was dropped and a new **--port** specification was added.

(made with skribilo)