Merge pull request #21 from Clinical-Genomics/dockerfile

Created a runnable Dockerfile

CHANGELOG.md

@@ -4,12 +4,11 @@ This change log will document the notable changes to this project in this file a
 
 ## [x.x.x]
 ### Added
-- Sample views 
+- Sample views
 - Batch views
+- Dockerfile
 
 ### Fixed
 
 ### Changed
 - Changed name of package to NIPTool
-
-

Dockerfile

@@ -0,0 +1,19 @@
+FROM python:3.8-slim
+
+LABEL base_image="python:3.8-slim"
+LABEL about.home="https://github.com/Clinical-Genomics/NIPTool"
+LABEL about.tags="NIPT,statistics,Non Invasive Prenatal Test,python"
+
+WORKDIR /home/worker/app
+COPY . /home/worker/app
+
+# Install app requirements
+RUN pip install -r requirements.txt
+
+# Install app
+RUN pip install -e .
+
+# Create and switch to a new non-root user
+RUN useradd worker
+RUN chown worker:worker -R /home/worker
+USER worker

README.md

@@ -30,16 +30,26 @@ nipt run
 ```
 And play around with the interface.
 
+### Docker image
+
+NIPTool can be runned also as a container. The image is available [on Docker Hub](https://hub.docker.com/repository/docker/clinicalgenomics/niptool) or can be build using the Dockerfile provided in this repository.
+
+To build a new image from the Dockerfile use the commands: `docker build -t niptool .`
+
+To run the image use the following command: `docker run --name niptool niptool nipt `
+
+To remove the container, type: `docker rm niptool`
+
 
 ## Release model
 NIPTool development is organised on a flexible Git "Release Flow" branching system. This more or less means that we make releases in release branches which corresponds to stable versions of NIPTool.
 
 ### Steps to make a new release:
 
-1) Create a release branch from master named `version_X.X.X` 
+1) Create a release branch from master named `version_X.X.X`
 2) Update change log with the new version.
 3) Update NIPTool/__init__.py with the new version.
-4) Make a PR to master, 
+4) Make a PR to master,
 	- Name PR `release version X.X.X`
 	- Justify if its a patch/minor/major version bump
 	- Paste the latest changelog to the text body
@@ -67,15 +77,15 @@ The database is loaded through the CLI with data generated by the [FluFFyPipe](h
 ## CLI
 The CLI has two base commands - load and run. The load command is for loading batch and sample data into the nipt database, and the run command is for running the web application.
 
-### Load 
+### Load
 
 
 ```
 Usage: nipt -c <config.yaml> load batch  [OPTIONS] ...
 ```
 
 
-  
+
 ### Run
 ```
 Usage: nipt run [OPTIONS] ...