Skip to content

Installation

Via Foundry's main server is located at https://viafoundry.com. Via Foundry can also be run as a standalone application using a docker container.

Prerequisites:

  • Via Scientific Access Keys
  • Via Scientific Docker Hub Access Keys
  • Two Separate SSL Certificates for foundry and foundry-apps (e.g. Let’s Encrypt)
  • Hard disk: 100-200GB (root)
  • 16-32 CPUs
  • 64-128 GB of memory.
  • e.g. AWS instance type m6i.4xlarge+, GCP VM type n2-standard-16+
  • Operating System: Ubuntu 22.04
  • 1-2TB EBS (AWS) / Persistent SSD Disk (GCP) mounted drive

Preparation Steps

Before you begin, it is recommended to follow these best practices:

  1. Create a user named viafoundry on the target machine.

  2. Configure the directory and perform the installation while logged in as the viafoundry user.

  3. Ensure that the default shell for the 'viafoundry' user is set to 'bash'. Use echo $SHELL to validate the current SHELL, if not, use chsh to update the SHELL to /bin/bash.

Software Dependencies for Pipeline Execution

In order to execute Via Foundry pipelines, you have to install and validate certain software dependencies into your host machine.

To enable proper pipeline execution, Nextflow should be installed into your host environment. Since most of our pipelines isolate their dependencies within their Docker, please install Docker or Podman into your machine by following the guidelines below. If your platform doesn't support the installation of Docker, you can still use our pipelines with just Singularity.

  • Installing Nextflow
  • Java v11+ (for nextflow)
  • Installing Docker
  • Installing Singularity (Version 3) (required when docker is not available)
  • AWS CLI v2 for AWS resources access
  • GCloud/GSUtil CLI for GCP resources access

How to Add Software to Your $PATH Environment:

  • JAVA Command (optional): If JAVA is not added to the $PATH environment, you can run the command (module load java/8.0) to manipulate your $PATH environment and gain access to JAVA.
  • Nextflow Path or Command (optional): If Nextflow is not added to the $PATH environment, you can either enter the path of the nextflow (eg. /project/bin), or run the command (module load nextflow) to manipulate your $PATH environment and gain access to new software.
  • Docker/Singularity Command (optional): You can run a command (eg. module load docker/1.0.0 or module load singularity/3.0.0) to manipulate your $PATH environment in order to gain access to new software.

Software Dependencies for Foundry Installation

  • Apache2 or NGINX (to redirect the site to selected domain)
  • Docker (latest version)

Installation

  1. We install the database and software outside of the container to be able to keep the changes in the database and software every time you start the container. Therefore, please choose a directory in your machine to mount. Then replace /path/to/mount with your path to create a directory. Please remove s permission from the directory for proper installation.

    chmod ug-s /path/to/mount
mkdir -p /path/to/mount

  2. Use docker to download Foundry container from a private ViaScientific repository.

    docker login
# username:viasdock
# password: will be sent with separate email
docker pull viascientific/vfoundry-docker

  3. Please execute the following command to start the container. Please don't change the target directory(/export) in the docker image and bind it to host port 8080.

    docker run -m 10G -p 8080:8080 --name vfoundry -v /path/to/mount:/export -dti viascientific/vfoundry-docker /bin/bash

  4. After you start the container, you need to start the mysql and apache server using the command below:

    startup (if this is for the initial setup time)
start.sh (if this is continuous maintenance after initial installation)

  5. Verify that foundry and mysql folders located inside of the export folder.

    ls /export

  6. Update software version by executing following commands in docker:

    cd /export/vsso && git pull && yarn install && yarn build && pm2 restart pm2-process.json
cd /export/vmeta && git pull && yarn install && yarn build && pm2 restart pm2-process.json
cd /export/vportal && git pull && yarn install && yarn build && pm2 restart pm2-process.json
cd /export/vfoundry && git pull && yarn install && yarn build && pm2 restart pm2-process.json
python /export/vpipe/scripts/updateDN.py

  7. Now, you can open your browser to access foundry using the URL below:

    http://localhost:8080