Galaxy-SARS-CoV-2-sequence-upload

This is a repository to build a Galaxy container which can be used to remove human traces from sequence reads, assemble genomes and to upload SARS-Cov-2 sequences (raw and assembled) to ENA.

The ENA raw reads uploading is based on the command line tool ena-upload-cli which is wrapped in following Galaxy tool.

Prerequisites

Docker

Make sure docker is installed and available on your path. For more information on how to install docker please visit this website.

ENA Webin

In order to upload to ENA, it is required to have the credentials of an ENA Webin account. A Webin can be made here if you don't have one already. The WEBIN_ID parameter makes use of the full username looking like: Webin-XXXXX. Visit Webin online to check on your submissions or dev Webin to check on test submissions.

Usage

Building the container image (optional)

This step is only needed when you want to build the container yourself. There is also a pre made image available on Quay.io, explained in the next section.

Build command:

docker build -t covid-19-upload -f Dockerfile .  

Running the container

Run the container from Quay.io:

Linux/windows:

docker run -p "8080:80" --privileged quay.io/galaxy/covid-19-upload

MacOS:

docker run -p "8080:80" quay.io/galaxy/covid-19-upload:hg38

Or run your built container (optional):

docker run -p "8080:80" --privileged covid-19-upload

The run command explained:

• -p "8080:80" will let the container host Galaxy on port 8080
• --privileged will allow the container to load a reference genome through CVMFS when needed

Your own galaxy instance is running

When the container is running (it can take some minutes to start all services), open a webbrowser and go to http://localhost:8080/. Normally you should see here the Galaxy interface. If "this page is not found", wait a little longer. Some general information will be found in the middle panel of the galaxy instance.

Setting up the credentials for a brokering account

1. Login as admin using admin as username and password as password, this will give you full access to the galaxy instance.
2. Go to user > preferences in the top navigation
3. Click on Manage information
4. Fill in the ENA Brokering account details
5. Click save

Example data

In the example directory an example Excel sheet can be found with example metadata along with example data files.

Tool documentation

Extensive documentation in how to use the tools inside the Galaxy container can be found here.

Acknowledgements

Special thanks to ENA and the lab of Björn Grüning for helping out with the tools used in this container