SMRT Link Dockerfile

This is a work in progress. It might not work yet.

This repository contains everything needed to get PacBio SMRT Link software running in a Docker container. The Dockerfile presented here builds a Docker image that contains SMRT Link. You don't need to download anything from here, just make sure you have a system that meets the minimum requirements and execute the commands below to build an image and run the container.

Host system

SMRTlink needs a big computer. Much bigger than laptops and most desktops. Here are the system requirements at present:

The recommended and minimum configurations are:
   Total Physical Memory:        64 GB (recommended), 32 GB (minimum)
   Total Number of Processors:   32    (recommended), 16    (minimum)
   Minimum open files limit   ('ulimit -n'):  8192  (required)
   Minimum user process limit ('ulimit -u'):  8192  (required)

Having less than the required limits will result in a warning, and by default installation will not complete if there are any warnings.

Amazon Web Services

I developed this Dockerfile on an m4.10xlarge EC2 instance, which exceeds the above recommended configuration, running Amazon Linux. I made the following changes to the default configuration:

• Increase the storage to 100 GB

• Open the following ports:

  • 9090-9095 (for SMRT Link services)

  • 8243 (for SMRT Link )

  • 443 (for git access via https during installation)

Once the instance is running, increase the open files limit. I took the approach presented at http://aws-labs.com/increase-open-files-limit/ Paste the following into /etc/security/limits.conf just before the line # End of file:

*         hard    nofile      500000
*         soft    nofile      500000
root      hard    nofile      500000
root      soft    nofile      500000

Reboot the amazon machine for the new settings to take effect. You can run ulimit -Sn to see if the limit was reset.

Now install docker with:

sudo yum update -y
sudo yum install -y docker
sudo yum install -y git
sudo service docker start
sudo usermod -a -G docker ec2-user

Log out and then log in again for the usermod changes to take effect.

Your Amazon machine is now ready to build and run the SMRTLink Docker container.

Build and run

To build the docker container, execute:

docker build --ulimit nofile=500000:500000 https://github.com/caseywdunn/docker-smrtlink.git#master:docker -t smrtlink:5.0.1.9585

If all goes well this will finish with the line Successfully built [id], where [id] is the image ID for the image you just built. You can then run a container based on this id with (substituting [id]):

docker run --ulimit nofile=500000:500000 [id]

To run the container interactively, eg to debug it, you can instead run:

docker run --ulimit nofile=500000:500000 -it [id] bash

Installation notes

The SMRT Link installation is done by the script /opt/pacbio/smrtlink/install/smrtlink-release_5.0.1.9585/admin/bin/installprompter. This script has a few options that can simplify installation:

• --batch executes it in non-interactive mode, so there are no user prompts

• --ignore-system-check will proceed with installation even if there is a warning during system check