Bug 511 – fiji on ubuntu : install problem when using apt-get

Bug 511 - fiji on ubuntu : install problem when using apt-get


Summary:	fiji on ubuntu : install problem when using apt-get

Status:	RESOLVED WONTFIX

Product:	Fiji
Classification:	Unclassified
Component:	Debian Packages
Version:	unspecified
Hardware:	PC Linux

Importance:	P3 blocker
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2012-10-11 14:30 CDT by pierre_henri puech
Modified:	2013-07-07 09:18 CDT
CC List:	4 users (show)

See Also:

Attachments
modified /usr/bin/fiji script (33 bytes, text/plain) 2013-01-20 10:26 CST, Egor Zindy

Description pierre_henri puech 2012-10-11 14:30:25 CDT

hi there
i'm trying to run fiji on ubuntu  12.04  and i tried to install it through the method you propose (apt-get) and once installed, fiji does not launch from the iconic menu (under gnome classic) and not even from the command line : i get the following message

php@php-workstation:~$ fiji
Re-executing with correct library lookup path
Found that JAVA_HOME was: '/usr/lib/jvm/java-6-openjdk/'
Could not launch system-wide Java (No such file or directory)

on the same computer, when using the targz way of intalling (decompressing + simply double clicking on the fiji-linux file) i get a nice and self upgrading fiji...

any idea ?
best
pierre-henri

Comment 1 Olivier Rodriguez 2012-10-29 17:20:23 CDT

Hi Pierre-Henri,

this worked fine in my case:
- backup fiji executable (e.g. in your home folder, just in case):
mkdir -p ~/bak ; sudo cp /usr/bin/fiji ~/bak
- edit /usr/bin/fiji in root mode:
gksudo gedit /usr/bin/fiji
- replace the following line:
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk/
by this one:
export JAVA_HOME=/usr/lib/jvm/java-6-openjdk-amd64/

I hope this will help!
Regards,
Olivier

Comment 2 pierre_henri puech 2012-11-12 12:35:07 CST

thanks !

Comment 3 Egor Zindy 2013-01-20 10:26:29 CST

Created attachment 90
modified /usr/bin/fiji script

I hit the same bug today trying to install fiji on Ubuntu 12.04 64 bit, using the apt-get instructions on http://fiji.sc/wiki/index.php/Downloads

I followed Olivier's instructions and thought a test in /usr/bin/fiji would be more appropriate?

This worked for me (see below). I attached my modified /usr/bin/fiji file.

Kind regards,
Egor


if [ -z "$JAVA_HOME" ]
then
    if [ -n "$FIJI_JAVA_HOME" ]
    then
        export JAVA_HOME=$FIJI_JAVA_HOME
    else
        if [ -d "/usr/lib/jvm/java-6-openjdk-amd64" ]
        then
            export JAVA_HOME=/usr/lib/jvm/java-6-openjdk-amd64/
        else
            export JAVA_HOME=/usr/lib/jvm/java-6-openjdk/
        fi
    fi
fi

Comment 4 fijibugzilla 2013-05-12 02:03:59 CDT

FWIW, even 32-bit java is not at /usr/lib/jvm/java-6-openjdk/ , but at /usr/lib/jvm/java-6-openjdk-i386/

As for the workaround, /usr/bin/fiji actually says that Fiji will preferably use JAVA_HOME, or "FIJI_JAVA_HOME (which may be set in /etc/default/fiji)". It's probably better to set these variables rather than modifying /usr/bin/fiji itself, as upgrades may break this in the future.

I'm not sure how to modify JAVA_HOME, but (as stated in the quote above) you can change FIJI_JAVA_HOME in /etc/default/fiji.

Comment 5 Johannes Schindelin 2013-07-07 09:18:05 CDT

Unfortunately, it was determined that it is too hard to maintain a Debian packaging set of Fiji. Please use the recommended way to install Fiji by unpacking the .tar.gz file linked at http://fiji.sc/Downloads and make sure that it is installed in a location where Fiji can update itself (e.g. the Desktop/).