Installation Guide

The following instructions guide the installation of the openVA Pipeline on Ubuntu 20.04 operating system.

Note

To make the installation process easier, all required software can be installed by downloading and running a bash script located in the main folder of the openVA_Pipeline repository:

• ubuntu_installation.sh

This script is valid for Ubuntu 20.04 and 22.04.

1. Install Python tools, OpenJDK, R, SQLite3, and SQLCipher by typing the following commands at a terminal prompt (indicated by $)

   $ sudo apt update
   $ sudo apt install python3-pip python3-venv openjdk-11-jdk r-base sqlite3 libsqlite3-dev sqlcipher libsqlcipher-dev curl libcurl4-openssl-dev -y
   

2. Configure OpenJDK with R by running the following command

   $ sudo R CMD javareconf
   

3. In a terminal, start R by simply typing R at the prompt, or use sudo R for system-wide installation of the packages. The necessary packages can be installed (with an internet connection) using the following command:

   > install.packages("openVA")
   

   Note that > in the previous command indicates the R prompt (not part of the actual command). This command may ask the user to select a CRAN mirror (choose a mirror close to your geographic location). After the installation of the packages has been completed, you can exit R with the following command:

   > q('no')
   

4. Python 3.8 is included in in Ubuntu 20.04 (and Python 3.10 comes with Ubuntu 22.04), but we still need to update the package installer, setup a virtual environment, and install the openva-pipeline package. These tasks can be accomplished at the terminal as follows:

   $ python3 -m venv venv
   $ source venv/bin/activate
   $ pip install --upgrade pip
   $ pip install --upgrade setuptools
   $ pip install openva-pipeline
   $ deactivate
   

   We can enter the virtual environment and import the openva-pipeline package with the following terminal commands:

   $ source venv/bin/activate
   $ python
   
   >>> import openva_pipeline as ovapl   # import package
   >>> help(ovapl)                       # access primary help file (hit q to exit)
   >>> help(ovapl.run_pipeline)          # access help file for a particular function
   >>> quit()                            # return to virtualenv terminal shell
   
   $ deactivate
   

5. Install DB Browser for SQLite with the commands (the following commands are taken from the sqlitebrowser GitHub repository):

   $ sudo apt install build-essential git-core cmake libsqlite3-dev qt5-default qttools5-dev-tools \
       libsqlcipher-dev qtbase5-dev libqt5scintilla2-dev libqcustomplot-dev qttools5-dev
   $ git clone https://github.com/sqlitebrowser/sqlitebrowser
   $ cd sqlitebrowser
   $ mkdir build
   $ cd build
   $ cmake -Dsqlcipher=1 -Wno-dev ..
   $ make
   $ sudo make install
   

Alternative Installation Options

Using Java JDK (instead of OpenJDK)

Instructions for installing JDK 11 on Linux can be found here. After installing JDK 11, run the following command at the terminal to properly configure R

$ sudo R CMD javareconf

and then install the R packages (as described above).