Installing Mendeley Reference Manager (Ubuntu)

When life gives you AppImages, you learn how to install software

As lots of lab members may tell you, Mendeley Reference Manager is very useful for reading, annotating and managing articles. But the newest version of Mendeley is only available as an AppImage.

If you don't mind using an older version, you can download the debian file from the NAS at NetBackup/norlab_documents/Old_version_mendeley/mendeleydesktop_1.19.8_for_ubuntu_22.04.deb

Download Mendeley, make it executable, add Mendeley to path

UBUNTU 22.04 : libfuse2 is needed to run AppImages. Ubuntu 22.04 doesn't have libfuse2 by default :

# ON UBUNTU 22.04
sudo apt install libfuse2

The /opt directory is a great place for installing Mendeley. Download the .AppImage available on Mendeley's website. Once the download is complete, open a terminal from where you downloaded Mendeley Reference manager.

# Create a folder in /opt to install Mendeley
sudo mkdir /opt/mendeley

# Copy inside /opt/mendeley
sudo cp mendeley-reference-manager-<version>-x86_64.AppImage /opt/mendeley/mendeley.AppImage
# Ex :
# sudo cp mendeley-reference-manager-2.75.0-x86_64.AppImage /opt/mendeley/mendeley.AppImage

# Make it executable
sudo chmod +x /opt/mendeley/mendeley.AppImage

# We will install the symlink in ~/.local/bin.
# This folder may be non-existent
mkdir -p ~/.local/bin
. ~/.profile

# Symlink to run Mendeley from the terminal
ln -s /opt/mendeley/mendeley.AppImage ~/.local/bin/mendeley

Extract files from the contents of the AppImage

The icon of mendeley is included in the AppImage. AppImages are some kind of bundled software, where running an AppImage mounts a folder with the content of the software. We can extract files from an AppImage with a pattern to get specific files (mendeley-reference-manager.desktop and mendeley-reference-manager.png, in our example). These files are extracted in $PWD/squashfs-root :

# Extract files from the AppImage
mendeley --appimage-extract mendeley-reference-manager.desktop
mendeley --appimage-extract **/**/**/**/512*/**/*.png
find squashfs-root/usr/ -type f -print0 | xargs -0 mv -t squashfs-root/
rm -rf squashfs-root/usr

# Move files inside an appropriate path, like `/opt/mendeley`
sudo mv $PWD/squashfs-root/mendeley-reference-manager.* /opt/mendeley/

# Delete squashfs-root
rmdir $PWD/squashfs-root

Add icons to system

Mendeley's icon can be found in the files we copeid from the AppImage. We will copy them inside ~/.local/share/icons/.

# Create the directory
mkdir ~/.local/share/icons

# Copy the mendeley icon inside our program icons
cp /opt/mendeley/mendeley-reference-manager.png ~/.local/share/icons/

# Update the icon cache
sudo update-icon-caches ~/.local/share/icons/*

Create Desktop Entry

We now need to create a Desktop Entry in order to include Mendeley in the list of applications that can be launched from the Activities Menu. Luckily for us, there is a Mendeley desktop file that we already copied from the AppImage. This desktop file can be found in /opt/mendeley/mendeley-reference-manager.desktop We can copy it in the appropriate directory :

cp /opt/mendeley/mendeley-reference-manager.desktop ~/.local/share/applications/mendeley.desktop

Inside ~/.local/share/applications/mendeley.desktop, change Exec=AppRun for :

Exec=/opt/mendeley/mendeley.AppImage

As with earlier configurations, we must update the desktop entries database :

sudo update-desktop-database ~/.local/share/applications

Done ! We can now run Mendeley Reference Manager directly from the Activities menu !