ubuntu_with_fiji.rec

Bootstrap:docker
From:ubuntu:latest


%runscript
	export MYHOME=/home/user
	$MYHOME/Fiji.app/ImageJ-linux64 "$@"

%post
    export MYHOME=/home/user
    mkdir $MYHOME
    apt-get update
    apt-get -y install wget unzip xvfb libxrender1 libxtst6 libxi6
    apt-get clean
    wget https://downloads.imagej.net/fiji/latest/fiji-linux64.zip
	unzip fiji-linux64.zip -d $MYHOME
	rm fiji-linux64.zip
	export PATH=$MYHOME/Fiji.app:$PATH 
	echo "export PATH=$MYHOME/Fiji.app:$PATH" >> "$SINGULARITY_ENVIRONMENT"
	cd $MYHOME
	echo 'print("Hello World!");' > helloWorld.ijm
	$MYHOME/Fiji.app/ImageJ-linux64 --update update

%test
	export MYHOME=/home/user
	export PATH=$MYHOME/Fiji.app:$PATH
	$MYHOME/Fiji.app/ImageJ-linux64 --headless -macro $MYHOME/helloWorld.ijm