Singularity container scanning with CoreOS Clair
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Merge pull request #7 from dctrud/singularity3.2


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You can also use your local clone with git send-email.


Scan Singularity container images for security vulnerabilities using CoreOS Clair.

The CoreOS Clair vulnerability scanner is a useful tool able to scan docker and other container formats for security vulnerabilities. It obtains up-to-date lists of vulerabilities for various platforms (namespaces) from public databases.

We can use Clair to scan singularity containers, by exploiting the fact that an exported .tar.gz of a singularity container image is similar to a single layer docker image.

This tool:

  • Exports a singularity image to a temporary .tar.gz file (this will be under $TMPDIR)
  • Serves the .tar.gz file via an in-built http server, so the Clair service can retrieve it
  • Calls the Clair API to ingest the .tar.gz file as a layer for analysis
  • Calls the Clair API to retireve a vulnerability report for this layer
  • Displays a simple text, or full JSON format report

Based on experiments detailed in this Gist


This tool should be considered proof of concept, not heavily tested. Use at your own risk.

There is no support yet for SSL client certificates to verify that we are sending API requests to a trusted Clair instance, or that only a trusted Clair instance can retrieve images from the inbuilt http server. This means that this solution is insecure except with an isolated local install of Clair.


To use clair-singularity you will need a Linux host with:

  • Python 2.7 or greater installed
  • Singularity 3+ installed (tested with 3.2.1) and the singularity executable in your PATH
  • A Clair instance running somewhere, that is able to access the machine you will run clair-singularity on. It's easiest to accomplish this using docker to run a local Clair instance as below.

Starting a local Clair instance

If you have docker available on your local machine, the easiest way to start scanning your Singularity images is to fire up a Clair instance locally, with docker. The official Clair docker images are a blank slate, and do not include any vulnerability information. At startup Clair will have to download vulnerability information from the internet, which can be quite slow. Images from github user arminc are available that include pre-seeded databases:

To startup a Clair instance locally using these instances:

docker run -d --name db arminc/clair-db:2019-06-24
docker run -p 6060:6060 --link db:postgres -d --name clair arminc/clair-local-scan:v2.0.8_0ed98e9ead65a51ba53f7cc53fa5e80c92169207

Replace the clair-db:2019-06-24 image tag with a later date for newer vulnerabilities


Clone the git repo, or download and extract the zip then:

python install


Clair on same machine

If you are running clair-singularity locally (outside of docker), and clair within docker, you need to tell clair-singularity to serve images on the main IP of your host, so that dockerized clair can access them.

To scan a singularity image, using a clair instance running under local docker, on port 6060:

clair-singularity --bind-ip myimage.img

/Replace with a non-localhost IP of your machine, accessible to docker containers./

Clair on a different machine

If clair is running on a different machine, you must use the --clair-uri option to specify the base URI to the clair instance, and the --bind-ip and/or --bind-port options to specify a public IP and port on this machine, that clair can access to retrieve images from clair-singularity.

clair-singularity --clair-uri --bind-ip= --bind-port=8088 myimage.img

Full JSON Reports

By default, clair-singularity gives a simplified text report on STDOUT. To obtain the full JSON report returned by Clair use the --jsoon-output option.

clair-singularity --json-output myimage.img

Development / Testing

Tests can are run in 3 different ways:

Local - no access to Clair

Runs all tests that don't depend on access to a Clair server, using the local Python.

$ build_scripts/

Local - dockerized with Clair

Starts a Clair service with local docker, builds clair-singularity into a docker container, with Python 3.5, and runs tests in this docker container.

$ build_scripts/


Travis CI automated testing will test non-Clair dependent code using Python 2.7, 3.6, 3.7

Clair dependent code will be tested only in the 3.6 environment, by building the docker container, starting a Clair service, and running tests in the docker container.