Installing on Linux

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.

Installation on Linux

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

bash ~/Downloads/jalview-2_11_2_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_2_0-linux_x64-java_8.sh
./jalview-2_11_2_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_2_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_2_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_2_0-linux_x64-java_8.sh -c

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

Console mode install on Linux

Unattended mode

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

./jalview-2_11_2_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_2_0-linux_x64-java_8.sh -q -dir ~/local/jalview

Unattended mode install on Linux

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

sys.installationDir=/Users/&lt;user&gt;/AppData/Local/Jalview
sys.fileAssociation.extensions$StringArray="jvp","jvl","amsa","annotations,jvannotations","biojson","blc","aln","txt","fa,fasta","features,jvfeatures","gb,gbk","gff2","gff3","concise,jnet","msf","pfam","phy","pileup","pir","rnaml","mat","stk,sto"
# you can also add file extensions "cif","mcif,mmcif","ent,pdb" which are not set by default
sys.fileAssociation.launchers$StringArray="JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW","JALVIEW"
sys.languageId=en
makeSymbolicLink$Boolean=true
createDesktopLinkAction$Boolean=true

If you remove or add file extensions to the sys.fileAssociation.extensions$StringArray, you must also remove or add the same number of launcher IDs ("JALVIEW") to the sys.fileAssociation.launchers$StringArray.

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

./jalview-2_11_2_0-linux_x64-java_8.sh -q -varfile mydefaults.varfile

Further details

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

or contact us on the Jalview Discussion Forum

Thanks to ej-technologies for granting a free install4j license to the Jalview Open Source Project. Jalview's desktop installers were built with the install4j multi-platform installer builder and Gradle.