stardist.rec

Bootstrap:docker
From:debian:buster-slim


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

%setup
    mkdir ${SINGULARITY_ROOTFS}/home/user

%files
    stardist_script.py /home/user

%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
    mkdir $MYHOME/Fiji.app/models
    wget https://data.broadinstitute.org/bbbc/BBBC001/BBBC001_v1_images_tif.zip
    unzip BBBC001_v1_images_tif.zip
    rm BBBC001_v1_images_tif.zip
    mv human_ht29_colon_cancer_1_images images    
    chmod 777 images
    $MYHOME/Fiji.app/ImageJ-linux64 --update add-update-site CSBDeep https://sites.imagej.net/CSBDeep/
    $MYHOME/Fiji.app/ImageJ-linux64 --update add-update-site StarDist https://sites.imagej.net/StarDist/
	$MYHOME/Fiji.app/ImageJ-linux64 --update update


%test
	export MYHOME=/home/user
	export PATH=$MYHOME/Fiji.app:$PATH
	$MYHOME/Fiji.app/ImageJ-linux64 --headless --ij2 --console --run $MYHOME/stardist_script.py