The COMBAT-SARS-CoV-2 Workbench is a all-included environment for SARS-CoV-2 genome data analysis. Users can load data and metadata, and run analyses including:
Data generated from these analyses can be used downstream or shared with databases like GISAID or NCBI's Genbank.
The workbench uses Docker and docker compose to hide the complexity of the software.
This setup was tested on a VM with the following specs.
Assumption :
docker
and docker-compose
installed on destination instance/VM.NOTE:
You can use scripts to install docker and deploy this stack.
ssh USER@REMOTE.SERVER
git clone https://github.com/COMBAT-SARS-COV-2/irida-galaxy-deploy.git ; cd irida-galaxy-deploy
docker-compose -f stack.yml up -d
NOTE:
This will take a couple of minutes.. :watch: :coffee:
Upon completion, point your browser to:
The default administrator username and password are:
admin:password1
for the main (IRIDA-based) web interfaceadmin:admin
for GalaxyWorkbench code is in GitHub - pvanheus/docker-galaxy-stable
git clone https://github.com/pvanheus/docker-galaxy-stable
cd docker-galaxy-stable/compose
docker-compose -f docker-compose.yml -f docker-compose.singularity.yml -f docker-compose.irida.yml up
cd docker-galaxy-stable/compose/galaxy-configurator/templates/irida/plugins
jar tf galaxy-configurator/templates/irida/plugins/sarscov2-artic-illumina-pipeline-plugin-0.1.10.jar
shed-tools install -g http://localhost:90 -a fakekey -t tools.yml