Dockerfile (Ubuntu, gedit, wget, git, PlantCV with examples)
The aim of this repository is to prepare a docker image for running PlantCV.
The following procedures are for Ubuntu 16.04 with Docker 17.12.0-ce installed
In the terminal:
sudo chmod u+x PlantCV_build.sh
sudo chmod u+x PlantCV_X11.sh
#Create a docker image plant_cv
./PlantCV_build.sh
#Create a container PlantCV using the docker image plant_cv
./PlantCV_X11.sh
The following procedures are for macOS 10.13.3 with Docker 17.12.0-ce installed
XQuartz: Preferences -> Security -> (Check) Allow connections from network clients
In the terminal:
sudo chmod u+x PlantCV_build.sh
sudo chmod u+x PlantCV_XQuartz.sh
#Create a docker image plant_cv
./PlantCV_build.sh
#Create a container PlantCV using the docker image plant_cv
./PlantCV_XQuartz.sh
The following procedures are for running Tutorial: VIS Image Pipeline.
Inside the container:
#Download the sample image from the tutorial
wget http://plantcv.readthedocs.io/en/latest/img/tutorial_images/vis/original_image.jpg -O /workspace/examples/input/sample0.jpg
#Run the VIS Pipeline tutorial
cd /workspace/examples
python vis_tutorial.py -i ./input/sample0.jpg -o ./output -r result.txt -w True
Outcomes are stored in /workspace/examples/output.
To exit the container, type exit.