MINERVA
Platform Documentation

Install#

How to install#

Debian/Ubuntu operating system#

Installation instructions are for Debian (tested on stretch, buster, bullseye, bookworm) and Ubuntu (tested on 16.04, 18.04, 20.04, 22.04).

Install MINERVA platform using the following command:

curl -s https://minerva.pages.uni.lu/scripts/install.sh -o minerva-install.sh; \
sudo bash minerva-install.sh; \
rm minerva-install.sh


Run MINERVA platform by entering: http://localhost:8080/minerva/ in the web browser.
Use the following admin credentials to log in to the admin panel:

login: admin
password: admin


Follow instructions in the Administrator manual to change the password and, if needed, to add new users.

Virtual Machine image#

You can download an image of a virtual machine running Debian Linux and a working instance of MINERVA platform using the following link. Choose the version you would like to try and download minerva-*_release.ova file.

Suggested tool to open and use is Oracle VM VirtualBox.

Once the VM is running, run MINERVA platform by entering: http://localhost:8080/minerva/ in the web browser of the VM.

Use the following admin credentials to log in to the admin panel:

login: admin
password: admin


In case you’d like to configure the VM, root credentials are

login: root
password: 123qweasdzxc

Docker#

We prepared a docker compose configuration. To make it running just clone the repository and start it:

git clone https://gitlab.lcsb.uni.lu/minerva/docker.git
cd docker
docker-compose up


Once the container is installed, run MINERVA platform by entering: http://localhost:8080/minerva/ in the web browser.

Use the following admin credentials to log in to the admin panel:

login: admin
password: admin

Migration from version 13.2.x and lower#

Minerva 14 and higher require Apache Tomcat 8. Previous versions could work on Apache Tomcat 7.

Debian/Ubuntu operating system#

Migration will be done automatically on Debian/Ubuntu systems.

Docker#

Pulling the newest version of docker-compose repository solves the tomcat8 dependency.

Database#

Currently MINERVA supports only postgresql database. We support versions 9.4>=,10.0>=, 11.0>=. Database can be configured in a /etc/minerva/db.properties file. This file should look like:

database.uri=jdbc:postgresql://host:port/database_name
database.username=database_user
database.password=database_password


where:

Database should be empty when MINERVA is starting for the first time. It will be automatically initialized. It’s also possible run MINERVA on database with content from the former version (but at least 12.1). In such situation migration to the new schema will happen automatically on tomcat start.

Logs#

Default MINERVA logs will be stored in ${sys:catalina.base}/logs/minerva.txt file, where ${sys:catalina.base} is tomcat home directory (typically it would be something like /var/lib/tomcat8/logs/minerva.txt). MINERVA uses log4j2 library as a logging mechanism. Logs can be customized by creating /etc/minerva/log4j2.properties file. Default configuration used by MINERVA is available here: log4j2.properties. More information how to configure log4j2 can be found on the library homepage.

Troubleshooting#

curl: command not found#

Usually curl should be installed on you machine. In case it is not, you can install it by yourself:

sudo apt install curl

update of minerva#

Minerva installed as debian package could be updated as other packages in your OS. You can manually trigger update of the minerva package:

sudo apt-get update
sudo apt-get --only-upgrade install minerva


If these commands do not update minerva on your machine then probably some tool overridden list of repositories on your machine (for example: puppet-agent). In such situation you can fix the list of repositories and update minerva by:

echo "deb https://repo-r3lab.uni.lu/debian/ stable main" | sudo tee /etc/apt/sources.list.d/repo-r3lab.list
sudo apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 0xcb185f4e31872412
sudo apt-get update
sudo apt-get --only-upgrade install  minerva

java installation#

Prior to minerva 13.0.0 Debian package installing minerva would install oracle java 8 and will make it a default version of a java running on Debian. So if you were using older version of java you might notice that something has changed. Currently minerva uses openjdk-8/openjdk-11.

Exported CellDesigner file#

Very rarely, generated CellDesigner files might be corrupted and cannot be opened using CellDesigner. We are aware of this and we are constantly working on updating the export function. If this error happens to you, please send us small examples so we can track problem faster.

Installation of debian package#

In case you have some problems with installing debian package (apt-get fails) you will be able to find more information in the log file:

/var/log/minerva-install.log

When minerva is working on tomcat8 the log file is located in:

/var/log/tomcat8/minerva.txt

You can also check tomcat8 logs:

/var/log/tomcat8/catalina.out

Since version 17 minerva does not depend on tomcat anymore and all logs are located in:

/var/log/minerva.txt

Performance#

On machines with heavy usage and many projects minerva might slow down significantly at some point. This might be caused by underlying database. It is recommended to run VACUUM full periodically (once a week when minerva is not used). Minerva cannot run vacuum full automatically because it locks and rewrites tables that can cause deadlocks and failure when uploading projects.

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