Jalview

Hello Jean-Christophe,

I hope you enjoyed your stay in Edinburgh and found the BioSysBio conference to be of use to you.

After our discussion I thought I'd let you know how to run Jalview from the command line.

Firstly you should download the latest version of Jalview from http://www.jalview.org/Web_Installers/install.htm
(You must install the InstallAnywhere version)

The command to start Jalview is

java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar jalview.bin.Jalview -open FILE_NAME

Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If using Windows, use backslash "\" instead of forward slash "/"

Replace FILE_NAME with the name of your file to open.

Hope this is of some use to you, please let us know if this could be improved.

Andrew Waterhouse

Crikey! That is a bit of a monster command-line. Is there any way that could be simplified?
G.

java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar

   jalview.bin.Jalview -open FILE_NAME

···

Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If using Windows, use backslash "\" instead of forward slash "/"

Replace FILE_NAME with the name of your file to open.

Crikey! That is a bit of a monster command-line. Is there any way that
could be simplified?

bash/csh/bat script that is written on install?

..d

···

On 18/7/05 5:25 pm, "Geoff Barton" <geoff@compbio.dundee.ac.uk> wrote:

G.

java -Djava.ext.dirs=JALVIEW_HOME/lib -cp JALVIEW_HOME/jalview.jar

   jalview.bin.Jalview -open FILE_NAME

Replace JALVIEW_HOME with the full path to Jalview Installation Directory. If
using Windows, use backslash "\" instead of forward slash "/"

Replace FILE_NAME with the name of your file to open.

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