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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 0 (tunnel)

You can use ssh tunneling to access mysql from your machine. Try something like:

ssh -L 3306: -f -N tux02.genenetwork.org
mysql -uwebqtlout -pwebqtlout -h db_webqtl -A -e "show tables;"

If you already have that port in use on your machine try

ssh -L 3307: -f -N tux02.genenetwork.org
mysql -uwebqtlout -pwebqtlout -h -P 3307 db_webqtl -A -e "show tables;"

To keep the connection alive add something like this to your `~/.ssh/config`

ServerAliveInterval 60
ServerAliveCountMax 10

For specific hosts you can set it up as

Host tux02
  HostName tux02.genenetwork.org
  TCPKeepAlive yes
  ServerAliveInterval 60
  user myname

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(!) Here we run a new database, but you can use an existing DB as was done in

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, for example

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

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

/export/mysql$ ~/opt/guix-pull/bin/guix shell mysql -- mysql --socket=var/run/mysqld/mysqld.sock -uwebqtlout -pwebqtlout db_webqtl


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)

To run/bind on a network interface we can open up with:

export TMPDIR=/tmp
mysqld_safe --datadir='/var/lib/mysql/' --port=3307 --user=$USER --group=users --nowatch --bind-address --socket=/var/run/mysqld/mysqld.sock

Test with

 ~/opt/guix-pull/bin/guix shell mysql -- mysql -uwebqtlout -pwebqtlout db_webqtl -h --port=3307

Please don't use world writeable bind-address If you run it for your own purposes use ssh tunneling instead (see above).

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)