Installing on Linux
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
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
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
In a Console or Terminal, change folder to where you downloaded the file and run it with
You will be able to make the same selections found in the graphical installer.
In a Console, change folder to where you downloaded the file and run it with the
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
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/<user>/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
sys.fileAssociation.extensions$StringArray, you must also remove or add the same number of launcher IDs (
"JALVIEW") to the
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
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