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omicsBroker is a tool to easily annotate and publish omics data to ENA (EBI database).

omicsBroker & Docker

The omicsBroker application was developed with Docker and the image containing R and all necessary libraries is available online (here). Using omicsBroker by this method guarantees reproducibility of the analyses.

Requirements

We use Docker to develop and manage omicsBroker. We invite you to verify that the following requirements are correctly satisfied before trying to bootstrap the application:

• Docker 1.12.6+

We recommend you to follow Docker's official documentations to install required docker tools (see links above).To help you, explanatory videos for each operating system are available here

Docker must be on for the duration of omicsBroker use.

Quick start

Have you read the "Requirements" section above?

Run application

Reminder : Docker must always be switched on for any installation and use of omicsBroker !

Step 1 : Open a terminal

• Windows
• mac OSX
• Linux

Step 2 : Run application

docker run --rm -p 3838:3838 --name omicsBroker tdenecker/omicsbroker

Note On linux, it may be necessary to use sudo (sudo docker run --rm -p 3838:3838 --name omicsBroker tdenecker/omicsbroker)

Step 3 - Open your favorite web browser

omicsBroker is running. You can open a web browser and use it in the following url : http://localhost:3838/.

omicsBroker & R

omicsBroker is available as an R package. You can install it as follows:

# install.packages('devtools', repos='https://cran.rstudio.com/', dependencies = TRUE)

library(devtools)
install_github('IFB-ElixirFr/omicsBroker')

omicsBroker::shiny_application(port = 3838, host = '0.0.0.0')

Warning : The packages may be different from those used during the development of the application. This method does not guarantee reproducibility.

omicsBroker & ShinyProxy

The limitation of the previous approaches is that the launch of the Shiny application is only done on a CPU. When several users are connected, performance drops sharply. One solution is to use Shinyproxy.

Shinyproxy is a java application that allows to deploy Shiny applications without any limit, either in number of applications or in number of users. The only limit is the resources you have at your disposal to run this service (CPU and RAM).

When the user connects to the Shinyproxy set up, the user chooses the application among the available Shiny applications. A container docker of the application is then launched and the user is redirected to the application.

This approach has been tested in an ubuntu 20.04 VM in the IFB cloud.

Download configuration files

mkdir shinyProxy
cd shinyProxy/

wget https://raw.githubusercontent.com/IFB-ElixirFr/omicsBroker/main/shinyProxy/Dockerfile
wget https://raw.githubusercontent.com/IFB-ElixirFr/omicsBroker/main/shinyProxy/application.yml

Build docker network

docker network create sp-network

Build docker Shinyproxy image

docker build -t shinyproxy .

Import omicsBroker image

docker pull tdenecker/omicsbroker

Run omicsBroker

sudo docker run -d -v /var/run/docker.sock:/var/run/docker.sock --net sp-network -p 443:80 shinyproxy

WARNING : The open port of the IFB cloud VMs is port 443 (which you can find in this part of command line -p 443:80). This port can change depending on the deployment location.

Open application

If this method has been used in the IFB cloud VMs, Shiny proxi is available at https://XXX.XXX.XXX.XXX:443 where XXX.XXX.XXX.XXX is the IP address of the VM.

Development

Debug

During development or if server crashes (gray screen), you will probably need to get all messages (errors, warnings and notifications) in the R terminal.

Does the problem persist? Post an Issues and we will try to find a solution!

Test modifications in Docker environnement

docker run -it -p 3838:3838 -v ABSOLUTE_PATH_TO_omicsBroker_FOLDER/inst/application:/home/ tdenecker/omicsbroker bash -c "R -e \"shiny::runApp('/home/', host='0.0.0.0', port=3838)\""

Connect to a R session

docker run -ti --rm tdenecker/omicsbroker R

Warning: nothing is saved in this session (package installation, ...)

Documentation

The application comes with a wiki to help you best when using it. It is available here. This wiki is currently being written.

Citation

If you use omicsBroker project, please cite us :

IFB-ElixirFr , omicsBroker, (2020), GitHub repository, https://github.com/IFB-ElixirFr/omicsBroker

Contributors

• Thomas Denecker (ORCID 0000-0003-1421-7641)
• Hélène Chiapello (ORCID 0000-0001-5102-0632)
• Jacques van Helden (ORCID 0000-0002-8799-8584)

Ressources & Documentations

• Genomic Standards Consortium : MIxS Checklist v5.0 and GitHub
• ENA submission : ENA: Guidelines and Tutorials

Contributing

Please, see the CONTRIBUTING file.

Contributor Code of Conduct

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms. See CODE_OF_CONDUCT file.

License

omicsBroker is released under the BSD-3 License. See the bundled LICENSE file for details.