Docker build fails due to hardcoded Clear Linux version

[maciejmotyka]

Hi, when trying to build docker image I got an error that is (I think) caused by lack of backward compatibility between the builder image (clearlinux:latest) and the pinned version Clear Linux that we are trying to install (CLEAR_VERSION=41780).
I presume there must have been some change introduced to the clearlinux:latest since you last updated the Dockerfile, which makes it incompatible with the OS version 41780.
After I changed to CLEAR_VERSION=42950 the build succeeded.

Here's the error.

$ docker build -t vcf2maf:main .

[+] Building 17.0s (6/13)                                                                              docker:default
 => [internal] load build definition from Dockerfile                                                             0.0s
 => => transferring dockerfile: 1.45kB                                                                           0.0s
 => [internal] load metadata for docker.io/library/clearlinux:latest                                             1.9s
 => [internal] load .dockerignore                                                                                0.0s
 => => transferring context: 2B                                                                                  0.0s
 => [internal] load build context                                                                                0.0s
 => => transferring context: 1.00kB                                                                              0.0s
 => [builder 1/4] FROM docker.io/library/clearlinux:latest@sha256:78a9f76be5297fe4455e29169cdd2f12f27e0e093468  11.7s
 => => resolve docker.io/library/clearlinux:latest@sha256:78a9f76be5297fe4455e29169cdd2f12f27e0e093468354933db7  0.0s
 => => sha256:78a9f76be5297fe4455e29169cdd2f12f27e0e093468354933db78f6921f6c50 1.23kB / 1.23kB                   0.0s
 => => sha256:ccaf55331ac4d8c815e158493959d73342d631d325badfb789e98d7f84d335b9 1.22kB / 1.22kB                   0.0s
 => => sha256:36b6bf15d1c7239e4e1b035b2e702340bd80352a5f0c117ee8a16200fc84f3c4 1.19kB / 1.19kB                   0.0s
 => => sha256:d8b446266af417203ddeabfe64ef9ec39bd9602c347380c3e611ddd70af07332 72.25MB / 72.25MB                 5.8s
 => => sha256:457f4d5b67f8e66ba8be9f3ca344480f0283e4837e4ce3bd6e1e8c9dfb3cd84a 214B / 214B                       0.6s
 => => extracting sha256:d8b446266af417203ddeabfe64ef9ec39bd9602c347380c3e611ddd70af07332                        5.7s
 => => extracting sha256:457f4d5b67f8e66ba8be9f3ca344480f0283e4837e4ce3bd6e1e8c9dfb3cd84a                        0.0s
 => ERROR [builder 2/4] RUN swupd os-install --no-progress --no-boot-update --no-scripts     --version 41780     3.3s
------                                                                                                                
 > [builder 2/4] RUN swupd os-install --no-progress --no-boot-update --no-scripts     --version 41780     --path /install_root     --statedir /swupd-state     --bundles os-core-update,which:                                              
0.488 Installing OS version 41780                                                                                     
2.163 Error: Mismatching formats detected when diagnosing 41780 (expected: 40; actual: 37)
Latest supported version to diagnose: 42950
3.004 
3.004 Installation failed
------
Dockerfile:5
--------------------
   4 |     ENV CLEAR_VERSION=41780
   5 | >>> RUN swupd os-install --no-progress --no-boot-update --no-scripts \
   6 | >>>     --version ${CLEAR_VERSION} \
   7 | >>>     --path /install_root \
   8 | >>>     --statedir /swupd-state \
   9 | >>>     --bundles os-core-update,which
  10 |     
--------------------

I can create a PR, but could you first check if the problem is reproducible at your end?

[maciejmotyka]

The tests pass.

$ perl tests/vcf2maf.t
1..6
ok 1
ok 2
STATUS: Running VEP and writing to: tests/test_b38.vep.vcf
ok 3
ok 4
STATUS: Running VEP and writing to: tests/test_b38.vep.vcf
ok 5
ok 6

$ perl tests/vcf2vcf.t
1..4
ok 1
ok 2
ok 3
ok 4

$ perl tests/maf2vcf.t
1..4
ok 1
ok 2
ok 3
ok 4