Building DockerFile fails at Stage 'Install CLIF binary''

**Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.2/docs/FAQ.md**: yes

Describe the issue: I am building the deep variant Dockerfile (v1.2) off the Databricks Runtime base image (Ubuntu 18.04). Run into issues at Stage ‘Install CLIF binary’, I get the error,

ModuleNotFoundError: No module named 'apt_pkg'

I see in the build-prereq.sh script this comment,

Build clif binary from scratch. Might not be ideal because it installs a bunch of dependencies, but this works fine when we used this in a Dockerfile because we don't do build-prereq.sh in the final image.

Please advise how to get around this when building your own Docker Image

Cheers,

William

Setup

• Operating system: Ununtu 18.04
• DeepVariant version: 1.2
• Installation method (Docker, built from source, etc.): Docker
• Type of data: (sequencing instrument, reference genome, anything special that is unlike the case studies?)

Steps to reproduce:

• Command:
• Error trace: (if applicable)

Does the quick start test work on your system? Please test with https://github.com/google/deepvariant/blob/r0.10/docs/deepvariant-quick-start.md. Is there any way to reproduce the issue by using the quick start?

Any additional context:

[williambrandler]

Not at this time. Are there specific dependencies in Ubuntu 20.04 that are required? Or an older version of DV that has been tested on 18.04?

Would also like some clarification on this statement to help me figure out what is going on,

Build clif binary from scratch. Might not be ideal because it installs a bunch of dependencies, but this works fine when we used this in a Dockerfile because we don't do build-prereq.sh in the final image.

[pichuan]

@williambrandler

The bazel: command not found line is likely ok because build-prereq.sh will plan to install bazel after that line.

curl: command not found - this might have happened here:

https://github.com/google/deepvariant/blob/r1.2/build-prereq.sh#L75

I’m surprised that at this point there isn’t curl, because it was installed here:

https://github.com/google/deepvariant/blob/r1.2/build-prereq.sh#L54

You can remove the > /dev/null from that line and see if it was installed currently.