Dockerfile for Scipion (focused on ELIXIR STEERS)

This repository has a Dockerfile recipe which prepares a docker image with Scipion + Xmipp plugin installed.

The way to build it is cloning the repository and building the image:

git clone https://github.com/inab/scipion-dockerfile
cd scipion-dockerfile
docker build -t scipion .

Once it is built, you have to fetch both the CEITEC layer1 workflow template (file workflow_ceitec_layer1.json.template) and OSCEM_metadata dataset.

wget https://workflowhub.eu/workflows/599/git/2/download/workflow_ceitec_layer1.json.template
wget -r -nH -np --cut-dirs=4 https://scipion.cnb.csic.es/downloads/scipion/data/tests/OSCEM_metadata/

Last, it is run through next command line (supposing XAUTHORITY environment variable is pointing to the right file):

chmod go+rw $XAUTHORITY
docker run --rm -ti \
  -v ./OSCEM_metadata:/OSCEM_metadata:ro \
  -v ./workflow_ceitec_layer1.json.template:/workflow_ceitec_layer1.json.template:ro \
  --volume="$XAUTHORITY:/home/mambauser/.Xauthority:rw" --net=host \
  --env="XAUTHORITY=/home/mambauser/.Xauthority" --env="DISPLAY" \
  scipion:latest \
  /home/mambauser/scipion/scipion3 template /workflow_ceitec_layer1.json.template \
  moviesPath=/OSCEM_metadata/movies filesPattern='*.tiff' \
  voltage=300 spherical=2.7 sampling=0.495 dosePerFrame=0.64 \
  gainPath='/OSCEM_metadata/gain.mrc' streamingImport=false