Deployment.md

Deployment instructions

You may follow these instructions to deploy OmicNavigator with Docker. All you need to start is the DockerDeploy dockerfile within this repository.

Create image and start the container

The DockerDeploy file contains instructions for creating an OmicNavigator (latest release) docker image from the opencpu/base:v2.2.11-2 image available from dockerhub. It also does a few other things, including adding our OmicNavigator demo study called RNAseq123. Execute the following code to create the image and start a container:

## create the image
docker build -t ondeploy -f DockerDeploy . 
## start the container
docker run --name onappdeploy -t -d -p 8004:8004 ondeploy

You can now open the app in your browser at http://localhost:8004/ocpu/library/OmicNavigator/ and select RNAseq123 from the study drop-down menu.

Add your custom package to the container

Your custom OmicNavigator studies (created by a call to OmicNavigator::exportStudy(study=yourstudy, type='tarball')) may be installed via the following approach:

First, copy your study tarball into the container and start a shell:

## copy to container 
docker cp YourOmicNavigatorStudy.tar.gz onappdeploy:/

## shell in
docker exec -it onappdeploy /bin/sh

After shelling in, you can run R CMD INSTALL on your ONstudy tarball, or you can start an interactive R session and install your OmicNavigator study bundle. For example, after starting an R session you can execute the following using the 'pak' package:

pak::pkg_install('./YourOmicNavigatorStudy.tar.gz', dependencies=T)

You can navigate to http://localhost:8004/ocpu/library/OmicNavigator/ and select your newly installed study from the dropdown menu to verify installation.

Expose your container

Procedures for the exposure of an OmicNavigator container to network traffic depend on the hosting environment and/or cloud provider. The usual server administration and operation considerations apply, such as security, port configuration, resource allocation, etc.