Linux X64/Aarch64 choice

From Jalview 2.11.3.0 we additionally offer an installer for Linux on Aarch64 platforms.

Linux runs on many different platforms, but nearly all desktop or laptop installations will use an Intel or X64 based platform, so if you are uncertain choose the X64 installer.

If you know you are running linux on an Aarch64 or ARM64 platform (e.g. a Raspberry Pi 4) then choose the Aarch64 installer.

If you are running linux on a different platform please see the Installing on Unix page.

Graphical Installer

The Jalview installer for Linux should be run from the command line. It may be necessary to make the SH file executable.

The installer will then guide you through the installation options. In most cases we recommend accepting the default options.

If you just want to run the graphical installer, download the SH file and from a console run

bash ~/Downloads/jalview-2_11_4_0-linux-x64-java_8.sh

If you have problems, you can make the SH file executable and run it directly with:

cd ~/Downloads
chmod a+rx ./jalview-2_11_4_0-linux-x64-java_8.sh
./jalview-2_11_4_0-linux-x64-java_8.sh

The last part of the installer, registering file associations, seems to take quite long on linux, so don’t worry if the installer seems to sit doing nothing for a couple of minutes!

Verifying the SHA256 checksum

The download page provides a SHA256 checksum that you might want to use to verify your download. To do this in Linux, open a console and use the command

sha256sum ~/Downloads/jalview-2_11_4_0-linux-x64-java_8.sh

The output checksum should match the checksum displayed on the download page.

Installing using the command line

The same SH file can be used on the command line to install Jalview if required. In this case we recommend making the SH file executable first:

cd ~/Downloads
chmod a+rx ./jalview-2_11_4_0-linux-x64-java_8.sh

Console mode

In a Console or Terminal, change folder to where you downloaded the file and run it with

./jalview-2_11_4_0-linux-x64-java_8.sh -c

You will be able to make the same selections found in the graphical installer.

Unattended mode

In a Console, change folder to where you downloaded the file and run it with the -q option

./jalview-2_11_4_0-linux-x64-java_8.sh -q

Optionally you can set the installation directory with the -dir option followed by the directory, e.g.

./jalview-2_11_4_0-linux-x64-java_8.sh -q -dir ~/local/jalview

Note that due to Jalview’s automatic updates it is best to install Jalview in the user’s own disk space.

Changing the defaults

To set different defaults for an installation (most useful when using unattended mode), please read install4j Help: Response Files.

The default response file values that you might want to change for a Jalview installation look like

# install4j response file for Jalview 2.11.4.0

# Installation location (for a non Administrator user install this should be in user-space)
#sys.installationDir=

# File associations, must be from the list given and can also include "cif","mcif,mmcif","ent,pdb"
sys.fileAssociation.extensions$StringArray="jvp","jvl","amsa","annotations,jvannotations","biojson","blc","aln","fa,fasta","features,jvfeatures","fc","gb,gbk","gff2","gff3","concise,jnet","msf","pfam","phy","pileup","pir","rnaml","mat","stk,sto"

# Create a desktop icon (non-Administrator mode only)
createDesktopLinkAction$Boolean=false

# Whether to make a symbolic link to the jalview.sh command line script (Linux/Unix only)
makeSymbolicLinkAction$Boolean=true

# Location of such a symbolic link. If left blank then a suitable location will be determined (e.g. ~/bin or /usr/local/bin).
#unixBinDir=

# Advanced options
advancedOptions$Boolean=false

# If advancedOptions is set to true then the following apply, otherwise they are ignored and defaults will be used
allowUserDefaultAppdirUpdates$Boolean=true
allowSetUserAppdirPath$Boolean=false
userAppdirPath=
allowInstallerAppdirUpdates$Boolean=false

To use your own defaults varfile run the installer with the -varfile option and the full path of the file, e.g.

sudo bash ./jalview-2_11_4_0-linux-x64-java_8.sh -q -varfile $(pwd)/mydefaults.varfile

Further details

If you need more information about using the installer on the command line please see

• install4j Help: Installer Modes
• install4j Help: Command Line Options For Generated Installers
• install4j Help: Response Files

or contact us on the Jalview Discussion Forum .

Administrator install

Installing Jalview as an Administrator user so that it can be used by all users of a Linux system is possible from Jalview 2.11.4.0 onwards. Please see Administrator install and Administrator install on Linux for more details.