Docker image doesn't build

[wojciech-galan]

I was unable to build a Docker image using the dockerfile from the repo (master branch)

Relevant part of the log:

Step 5/7 : RUN     apt update     && apt install -yq --no-install-recommends         ca-certificates build-essential cmake curl wget git         zlib1g-dev libbz2-dev liblzma-dev libncurses5-dev libcurl4-gnutls-dev         libssl-dev libffi-dev         libreadline8 libreadline-dev sqlite3 libsqlite3-dev file         python3-all-dev python3-venv python3-pip python3-setuptools     && update-alternatives --install /usr/bin/python python /usr/bin/python3 10     && apt-get clean && rm -rf /var/lib/apt/lists/*
 ---> Running in f08aff4fa725

WARNING: apt does not have a stable CLI interface. Use with caution in scripts.

Ign:1 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64  InRelease
Err:2 https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64  Release
  Certificate verification failed: The certificate is NOT trusted. The certificate issuer is unknown.  Could not handshake: Error in the certificate verification. [IP: 152.199.20.126 443]
Get:3 http://archive.ubuntu.com/ubuntu focal InRelease [265 kB]
Get:4 http://security.ubuntu.com/ubuntu focal-security InRelease [128 kB]
Get:5 http://security.ubuntu.com/ubuntu focal-security/universe amd64 Packages [1270 kB]
Get:6 http://archive.ubuntu.com/ubuntu focal-updates InRelease [128 kB]
Get:7 http://archive.ubuntu.com/ubuntu focal-backports InRelease [128 kB]
Get:8 http://archive.ubuntu.com/ubuntu focal/multiverse amd64 Packages [177 kB]
Get:9 http://archive.ubuntu.com/ubuntu focal/restricted amd64 Packages [33.4 kB]
Get:10 http://archive.ubuntu.com/ubuntu focal/universe amd64 Packages [11.3 MB]
Get:11 http://security.ubuntu.com/ubuntu focal-security/restricted amd64 Packages [3928 kB]
Get:12 http://security.ubuntu.com/ubuntu focal-security/multiverse amd64 Packages [30.9 kB]
Get:13 http://security.ubuntu.com/ubuntu focal-security/main amd64 Packages [3937 kB]
Get:14 http://archive.ubuntu.com/ubuntu focal/main amd64 Packages [1275 kB]
Get:15 http://archive.ubuntu.com/ubuntu focal-updates/multiverse amd64 Packages [33.5 kB]
Get:16 http://archive.ubuntu.com/ubuntu focal-updates/universe amd64 Packages [1555 kB]
Get:17 http://archive.ubuntu.com/ubuntu focal-updates/main amd64 Packages [4399 kB]
Get:18 http://archive.ubuntu.com/ubuntu focal-updates/restricted amd64 Packages [4079 kB]
Get:19 http://archive.ubuntu.com/ubuntu focal-backports/main amd64 Packages [55.2 kB]
Get:20 http://archive.ubuntu.com/ubuntu focal-backports/universe amd64 Packages [28.6 kB]
Reading package lists...
E: The repository 'https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64  Release' does not have a Release file.
The command '/bin/bash -o pipefail -c apt update     && apt install -yq --no-install-recommends         ca-certificates build-essential cmake curl wget git         zlib1g-dev libbz2-dev liblzma-dev libncurses5-dev libcurl4-gnutls-dev         libssl-dev libffi-dev         libreadline8 libreadline-dev sqlite3 libsqlite3-dev file         python3-all-dev python3-venv python3-pip python3-setuptools     && update-alternatives --install /usr/bin/python python /usr/bin/python3 10     && apt-get clean && rm -rf /var/lib/apt/lists/*' returned a non-zero code: 100

The problem is certificate validation.
I was able to overcome it with

RUN rm /etc/apt/sources.list.d/cuda.list
RUN apt-key del 7fa2af80
RUN apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/3bf863cc.pub

before apt-update. Unfortunatelly then build failed on the last step:

Cannot import pyabpoa, some features may not be available.
Cannot import wurlitzer, some features may not be available.
make: *** [Makefile:158: check_lfs] Error 1
The command '/bin/bash -o pipefail -c cd /tmp/medaka     && make install_root     && cd /     && rm -rf /tmp/medaka' returned a non-zero code: 2

[cjw85]

The Dockerfile could admittedly do with some love. It has be removed in the latest release of the code due to the fairly integral change from tensorflow to pytorch in medaka v2.0.0. We will provide a docker image in due course.