Unable to build docker image from source due to multiple reasons

[sushruta]

I am trying to build the docker image of deepvariant but running into problems. I'm on r1.7 branch and my branch is up to date. I am also facing the same issues on r1.6.1 branch as well. The command I am using is the following -

docker build --build-arg=FROM_IMAGE=nvidia/cuda:11.8.0-cudnn8-devel-ubuntu22.04 \
             --build-arg=DV_GPU_BUILD=1 \
             -t deepvariant_gpu .

I am building this docker image on my laptop (M3 macbook).

PackagesNotFoundError error

The first error I get is -

1.247 Platform: linux-aarch64
1.247 Collecting package metadata (repodata.json): ...working... done
6.190 Solving environment: ...working... failed
6.260
6.260 PackagesNotFoundError: The following packages are not available from current channels:
6.260
6.260   - bioconda::samtools==1.15
6.260   - bioconda::bcftools==1.15
6.260

I resolved this error by removing the version numbers. i.e., removed the ==1.15 from both the lines

Error in the build-prerunreq.sh script

Once, I cross the previous error, I get this error -

 > [builder 6/6] RUN ./build-prereq.sh   && PATH="${HOME}/bin:/usr/local/nvidia/bin:/usr/local/cuda/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin" ./build_release_binaries.sh  # PATH for bazel:
0.101 ========== This script is only maintained for Ubuntu 22.04.
0.101 ========== Load config settings.
0.103 ========== [Thu Oct 31 21:28:00 UTC 2024] Stage 'Install the runtime packages' starting
0.104 ========== This script is only maintained for Ubuntu 22.04.
0.104 ========== Load config settings.
0.105 ========== [Thu Oct 31 21:28:00 UTC 2024] Stage 'Misc setup' starting
1.955 W: GPG error: https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/sbsa  InRelease: At least one invalid signature was encountered.
1.955 E: The repository 'https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2204/sbsa  InRelease' is not signed.
1.955 W: GPG error: http://ports.ubuntu.com/ubuntu-ports jammy InRelease: At least one invalid signature was encountered.
1.955 E: The repository 'http://ports.ubuntu.com/ubuntu-ports jammy InRelease' is not signed.
1.955 W: GPG error: http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease: At least one invalid signature was encountered.
1.955 E: The repository 'http://ports.ubuntu.com/ubuntu-ports jammy-updates InRelease' is not signed.
1.955 W: GPG error: http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease: At least one invalid signature was encountered.
1.955 E: The repository 'http://ports.ubuntu.com/ubuntu-ports jammy-backports InRelease' is not signed.
1.955 W: GPG error: http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease: At least one invalid signature was encountered.
1.955 E: The repository 'http://ports.ubuntu.com/ubuntu-ports jammy-security InRelease' is not signed.
------
Dockerfile:50
--------------------
  49 |
  50 | >>> RUN ./build-prereq.sh \
  51 | >>>   && PATH="${HOME}/bin:${PATH}" ./build_release_binaries.sh  # PATH for bazel
  52 |
--------------------
ERROR: failed to solve: process "/bin/sh -c ./build-prereq.sh   && PATH=\"${HOME}/bin:${PATH}\" ./build_release_binaries.sh  # PATH for bazel" did not complete successfully: exit code: 100

Looks like the repositories are either old or the sign has expired.

How to fix this error?