Support for Docker and Singularity (#24)

* Support for Docker and Singularity

* Rephrasing of certain sentences for a better clarity of meaning.

.dockerignore

@@ -0,0 +1,23 @@
+**/__pycache__
+**/.classpath
+**/.dockerignore
+**/.env
+**/.project
+**/.settings
+**/.toolstarget
+**/.vs
+**/.vscode
+**/*.*proj.user
+**/*.dbmdl
+**/*.jfm
+**/bin
+**/charts
+**/docker-compose*
+**/compose*
+**/Dockerfile*
+**/node_modules
+**/npm-debug.log
+**/obj
+**/secrets.dev.yaml
+**/values.dev.yaml
+README.md

Dockerfile

@@ -0,0 +1,16 @@
+FROM nvidia/cuda:11.3.1-devel-ubuntu20.04
+
+WORKDIR /app
+COPY . .
+
+RUN apt update
+RUN apt install -y git
+RUN apt install -y libfftw3-dev
+RUN apt install -y g++
+RUN apt install -y python3
+RUN apt install -y python3-pip
+RUN export CXX=$(which g++)
+RUN export CUDACXX=$(which nvcc)
+RUN git submodule update --init --recursive
+RUN pip install .
+

README.md

@@ -79,6 +79,42 @@ To run the tests, follow the installation instructions for developers and then d
 pytest
 ```
 
+## Docker
+
+Parakeet can also be installed and used via Docker (https://www.docker.com/get-started). To download parakeet's docker container you can do the following:
+
+```sh
+docker pull quay.io/rosalindfranklininstitute/parakeet:master
+```
+
+To use parakeet with docker with GPU support the host machine should have the approprate Nvidia drivers installed.
+
+To easily input and output data from the container the volume mechanism can be used, where a workspace directory of the host machine is mounted to a directory in the container (in the folder /mnt in the example below). For this reason it is advised that all the relevent files (e.g. config.yaml, sample.h5, etc.) should be present in the host workspace directory.
+
+Below is an example on how to use parakeet with docker to simulate the exit wave:
+
+```sh
+docker run --gpus all -v <host_workspace>:/mnt --rm -i -t parakeet:master parakeet.simulate.exit_wave -c /mnt/config.yaml -d gpu -s /mnt/sample.h5 -e /mnt/exit_wave.h5
+```
+
+## Singularity
+
+Parakeet can also be installed and used via Singularity (https://sylabs.io/guides/2.6/user-guide/installation.html). To download parakeet's singularity container you can do the following:
+
+```sh
+singularity pull library://rosalindfranklininstitute/parakeet/parakeet:master
+```
+
+Again similar to docker, to use parakeet with singularity and GPU support, the host machine should have the approprate Nvidia drivers installed.
+
+To easily input and output data from the container, a workspace directory in the host machine, where all the relevent files (e.g. config.yaml, sample.h5, etc.) should be present, can be binded to a directory in the container.
+
+Below is an example on how to use parakeet with singularity to simulate the exit wave:
+
+```sh
+singularity run --nv --bind <host_workspace>:/mnt parakeet.sif parakeet.simulate.exit_wave -c /mnt/config_new.yaml -d gpu -s /mnt/sample.h5 -e /mnt/exit_wave.h5
+```
+
 ## Usage
 
 Simulation of datasets is split into a number of different commands. Each