path on linux

[Benoit Zuber]

Hi,

On linux, if I am in ImageJ directory when I start it then all the
plugins are accessible. However when I start it from another directory
(with path/run), I don't get the plugins anymore. I tried the command :
path/run -ijpath path
but it did not help.
Could anybody please help me with this?
Thanks

Ben
--
Benoit Zuber
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH
UK

[Gabriel Lapointe]

This is my launching script that I've been using on Ubuntu and Debian
linux. I can start it in any directories and use the plugins
(-Dplugins.dir parameter). The only glitch is the LUT folder, it need to
be in the launching directory to be available.

Good luck,
Gabriel

#!/bin/bash
memory=7500m
imagej=/usr/local/ImageJ/ij.jar
java=/usr/lib/jvm/java-6-sun/jre/bin/java
javarun=/usr/lib/jvm/java-6-sun/lib/tools.jar
$java -Dplugins.dir=$HOME/.ImageJ/plugins -Xmx$memory -cp
$imagej:$javarun ij.ImageJ



Benoit Zuber wrote:

> Hi,
>
> On linux, if I am in ImageJ directory when I start it then all the
> plugins are accessible. However when I start it from another directory
> (with path/run), I don't get the plugins anymore. I tried the command :
> path/run -ijpath path
> but it did not help.
> Could anybody please help me with this?
> Thanks
>
> Ben
>  

[dscho]

Hi,

On Tue, 22 Sep 2009, Benoit Zuber wrote:

> On linux, if I am in ImageJ directory when I start it then all the
> plugins are accessible. However when I start it from another directory
> (with path/run), I don't get the plugins anymore. I tried the command :
> path/run -ijpath path but it did not help.

I usually try to avoid sending two Fiji advertisement mails out on the
same day, but you probably missed my other one:  One of Fiji's principal
missions is to overcome issues such as yours.

You can call Fiji from anywhere, even install a symbolic link in $HOME/bin
or wherever you like, and it will still find the plugins.  You are welcome
to copy your own plugins to the plugins directory, but of course, you can
also use the more convenient Plugins>Install Plugin... menu item.

To try it, just download Fiji for your platform from
http://pacific.mpi-cbg.de/, extract it, run Help>Update Fiji and restart
(the updating is necessary because a lot has been improved since end of
April, when the current version of Fiji was released).

Hth,
Johannes

[Vera, Pedro L.]

Johannes wrote:

>To try it, just download Fiji for your platform from
>http://pacific.mpi-cbg.de/, extract it, run Help>Update Fiji and restart
>(the updating is necessary because a lot has been improved since end of
>April, when the current version of Fiji was released).

Hello:
This is a bit off-thread, but I downloaded and installed the debian version of fiji. I don't see the option to do a general update from the Help menu. I just see Update menus? Is that what you meant or is there another way to do an update/upgrade of the entire program?
thanks

Pedro

[dscho]

Hi Pedro,

please Cc: me if you reply to me; I almost missed your mail between the
other 100 I got today.

On Wed, 23 Sep 2009, Vera, Pedro L. wrote:

> Johannes wrote:
>
> >To try it, just download Fiji for your platform from
> >http://pacific.mpi-cbg.de/, extract it, run Help>Update Fiji and
> >restart (the updating is necessary because a lot has been improved
> >since end of April, when the current version of Fiji was released).
>
> This is a bit off-thread, but I downloaded and installed the debian
> version of fiji. I don't see the option to do a general update from the
> Help menu. I just see Update menus? Is that what you meant or is there
> another way to do an update/upgrade of the entire program?

The Debian version of Fiji is installed via apt-get, and is also meant to
be updated that way.

Ciao,
Johannes

[Benoit Zuber]

Thanks Gabriel and Johannes for your reply!
Using a similar startup script as you described Gabriel worked well for me.
Regards,
Ben
Gabriel Lapointe wrote:

> This is my launching script that I've been using on Ubuntu and Debian
> linux. I can start it in any directories and use the plugins
> (-Dplugins.dir parameter). The only glitch is the LUT folder, it need to
> be in the launching directory to be available.
>
> Good luck,
> Gabriel
>
> #!/bin/bash
> memory=7500m
> imagej=/usr/local/ImageJ/ij.jar
> java=/usr/lib/jvm/java-6-sun/jre/bin/java
> javarun=/usr/lib/jvm/java-6-sun/lib/tools.jar
> $java -Dplugins.dir=$HOME/.ImageJ/plugins -Xmx$memory -cp
> $imagej:$javarun ij.ImageJ
>
>
>
> Benoit Zuber wrote:
>  
>> Hi,
>>
>> On linux, if I am in ImageJ directory when I start it then all the
>> plugins are accessible. However when I start it from another directory
>> (with path/run), I don't get the plugins anymore. I tried the command :
>> path/run -ijpath path
>> but it did not help.
>> Could anybody please help me with this?
>> Thanks
>>
>> Ben
>>  
>>    

--
Benoît Zuber
MRC Laboratory of Molecular Biology
Hills Road
Cambridge
CB2 0QH
United Kingdom
[phone]
[hidden email]