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A Singularity container for the ST Spot Detector WebApp

This document details how to get set up and running with the ST Spot Detector inside a singularity container.

Singularity can be found here: http://singularity.lbl.gov/

To install Singularity, follow the instructions on the following webpage relevant to your operating system:

Installation instructions

Start Vagrant

vagrant init singularityware/singularity-2.4
vagrant up
vagrant ssh

Update apt

sudo apt update

Install debootstrap

sudo apt-get install debootstrap

Once Singularity has been installed, you need to create a container:

singularity create --size 16384 st_aligner.img

Now clone the repository to get the container

git clone https://github.com/SpatialTranscriptomicsResearch/st_spot_detector_singularity.git

Once the container has been created, it can be bootstrapped with the bootstrap recipie provided. This command needs to be run as root in order to install all the components into the container.

sudo singularity bootstrap st_aligner.img st_spot_detector_singularity/st_aligner_bootstrap

Once the bootstrap procedure has finished (may take around 30 minutes), you are ready to run the st_aligner.

singularity run st_aligner.img

Accessing the webserver and other considerations

If you are running the container outside a virtual machine, you should be able to connect to it with the following address in your web browser:

  • localhost:8080

If you are running the container inside a virtual machine then a few additional steps are necessary.

First exist Vagrant

exit

Edit your Vagrantfile so that the following lines are uncommented (The file should be wherever you started Vagrant):

config.vm.network "forwarded_port", guest: 80, host: 8080, host_ip: "127.0.0.1"
config.vm.network "private_network", ip: "192.168.33.10"

config.vm.provider "virtualbox" do |vb|

	vb.memory = "16384"

end

Note that you may want to increase the memory if your images are very large.

Then reload Vagrant:

vagrant reload

Now enter Vagrant and reload the image:

vagrant ssh
singularity run st_aligner.img

This will allow you to connect to the webserver on the ip specified, on port 8080. Enter the following in your web browser:

  • 192.168.33.10:8080

The ST Spot Detector requires around 16GB of RAM. Less RAM is required if the images are reduced in size prior to aligning them. If you get the message "An error has occurred" while uploading images it is likely that the web server has run out of RAM. Either resize the input images, or allocate more RAM to your virtual machine (or both).