In ergonyc/omicser: NDCN Omics Browser

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Introduction

This document describes how the docker container was created and how to use it.

Dockerfile

The Dockerfile was created with golem::add_dockerfile(). This generates a Dockerfile with install commands for (almost) all R packages. The generated Dockerfile was used as basis to create the final Dockerfile.

Packages added manually:

• shinyFiles

Python environment

To create the python environment a small R script was developed (based on installation instruction of omicser). This file is copied into the container and executed during build of the container.

To make sure the correct python environment is used, an .Renviron file was created which uses an environment from reticulate to force the correct python environment. The .Renviron file is copied and copied to the correct location during build of the container.

App configuration

The omicser app needs a config file (app_config.yml) to run. For now a config file is already prepared and copied into the container and copied to the correct location. In the app_config.yml you need the database names set correctly for your system. The other parameters you should not need to change!

File locations

All the additional files needed to create the docker container or in folder docker_stuff.

• .Renviron
• app_config.yml
• install_py_env.R

Databases

The current setup leaves the database files outside the container. During start up of the container the location of the database files need to be coupled to the database folder inside the container.

Usage

Build docker container

The location of the Dockerfile needs to be the root of your project folder. Build the container with:

docker build --tag omicser_container .

Run the docker container

Run the container as follows:

docker run -d -p 3939:3939 -v /my_location/of/databases/:/root/DB/ omicser_container

ergonyc/omicser documentation built on June 15, 2022, 3:02 p.m.