Add more than one update site via commandline

updater
update-sites
Tags: #<Tag:0x00007fd542889e28> #<Tag:0x00007fd542889928>

#1

Hi guys,

is it possible to add more than one update site from the commandline using:

./ImageJ-<platform> --update add-update-site MySite http://mysite/

or can this only doen one-by-one.

And do I need to start ImageJ at the end to really apply the updates or is that done automatically?

Sebi


#2

Hi @sebi06,

you can to ./ImageJ-<platform> --update update to update from the commandline/terminal.

I don’t think it’s currently possible.

Best,
Stefan


#3

Thanks for the help. So I will do one by one. But I noticed that does not work for all the desired updates sites. Some them errors when adding them via the commandline


#4

What are the exact commands you’re invoking? And what are the error messages?


#5

Hi Jan, I think the error occured when trying to update Java8, CMP-BIA tools and MOASIC tools via command line. That’s why I commented them out.

Sebi

#
# Fiji + Java 8 Dockerfile
#

# Pull base JDK-8 image.
FROM java:8-jre

# Install Fiji.
RUN curl -O https://downloads.imagej.net/fiji/latest/fiji-linux64.zip
RUN unzip fiji-linux64.zip

ENV PATH $PATH:/Fiji.app/

COPY . .

RUN ls

# add Fiji-Update sites
#RUN ./Fiji.app/ImageJ-linux64 --update add-update-site Java-8 http://sites.imagej.net/Java-8/
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site BAR http://sites.imagej.net/Tiago/
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site BASIC http://sites.imagej.net/BaSiC/
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site BIG-EPFL http://sites.imagej.net/BIG-EPFL/
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site BioVoxxel http://sites.imagej.net/BioVoxxel/
#RUN ./Fiji.app/ImageJ-linux64 --update add-update-site CMP-BIA tools http://sites.imagej.net/CMP-BIA/
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site IBMP-CNRS http://sites.imagej.net/Mutterer/
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site IJPB-plugins http://sites.imagej.net/IJPB-plugins/
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site ImageScience http://sites.imagej.net/ImageScience/
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site IMCF Uni Basel http://sites.imagej.net/UniBas-IMCF/
#RUN ./Fiji.app/ImageJ-linux64 --update add-update-site MOSAIC ToolSuite http://mosaic.mpi-cbg.de/Downloads/update/Fiji/MosaicToolsuite
RUN ./Fiji.app/ImageJ-linux64 --update add-update-site PTBIOP http://biop.epfl.ch/Fiji-Update
RUN ./Fiji.app/ImageJ-linux64 --ij2 --headless --update update
#RUN ./Fiji.app/ImageJ-linux64 --ij2 --headless --console

RUN mv ./Fiji.app/jars/bio-formats/formats-common-5.1.10.jar ./Fiji.app/jars/bio-formats/formats-common-5.1.10.jar.old

CMD './Run_GuidedAcq_ROI.sh'

#6
[WARNING] Could not update from site 'IMCF': java.net.MalformedURLException: no protocol: Uni/db.xml.gz

Could you try to remove spaces from the names, @sebi06?


#7

The command line updater returns 1 if you try to add an update site that is already there (which is the case for Fiji). I’d just get rid of that line, the rest should work if you remove spaces.


#8

You mean I should use

IMCFUniBasel

instead of

IMCF Uni Basel

That is it?


#9

That and removing the line where you add the Java-8 update site has worked for me. Of course, I couldn’t run the script but everything else went smoothly…


#10

Did it work for you @sebi06?


#11

Yes. Thanks again. Now i have running docker container with an up to date Fiji plus update sites.