Podman can't build devcontainer

[gdevenyi]

System (complete the following information, else the issue will be closed):

• OS: CachyOS (I use ARCH btw..)
• Python: N/A
• nf-core: document how to check in template please
• nf-neuro HEAD

Describe the bug
devops devcontainer fails to build on apt key issues

To Reproduce
Steps to reproduce the behavior:

Start vscode without a built devcontainer

Expected behavior
works

Additional context
Add any other context about the problem here.

[142 ms] Dev Containers 0.454.0 in VS Code 1.116.0 (560a9dba96f961efea7b1612916f89e5d5d4d679).
[140 ms] Start: Resolving Remote
[148 ms] Setting up container for folder or workspace: /home/gdevenyi/projects/nf-neuro
[148 ms] Host: unix:///run/user/1000/podman/podman.sock
[151 ms] Start: Check Docker is running
[151 ms] Start: Run: podman version
[175 ms] Client:       Podman Engine
Version:      5.8.2
API Version:  5.8.2
Go Version:   go1.26.2-X:nodwarf5
Git Commit:   5b263b5f5b48004a87caac44e67349a8266d9ef4
Built:        Wed Apr 15 10:52:15 2026
OS/Arch:      linux/amd64
[178 ms] Start: Run: podman volume ls -q
[216 ms] Start: Run: podman ps -q -a --filter label=vsch.local.folder=/home/gdevenyi/projects/nf-neuro --filter label=vsch.quality=stable
[271 ms] Start: Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/gdevenyi/projects/nf-neuro --filter label=devcontainer.config_file=/home/gdevenyi/projects/nf-neuro/.devcontainer/devops/devcontainer.json
[327 ms] Start: Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/gdevenyi/projects/nf-neuro
[382 ms] Start: Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/gdevenyi/projects/nf-neuro
[434 ms] Running Dev Containers CLI:   up --user-data-folder /home/gdevenyi/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --docker-path podman --docker-compose-path podman-compose --container-session-data-folder /tmp/devcontainers-f739ce91-e207-4b02-95c0-d7fffd1b80271776955475033 --workspace-folder /home/gdevenyi/projects/nf-neuro --workspace-mount-consistency cached --gpu-availability detect --id-label devcontainer.local_folder=/home/gdevenyi/projects/nf-neuro --id-label devcontainer.config_file=/home/gdevenyi/projects/nf-neuro/.devcontainer/devops/devcontainer.json --log-level debug --log-format json --config /home/gdevenyi/projects/nf-neuro/.devcontainer/devops/devcontainer.json --default-user-env-probe loginInteractiveShell --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root --include-configuration --include-merged-configuration
[435 ms] Start: Run: /opt/visual-studio-code/code /home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /home/gdevenyi/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --docker-path podman --docker-compose-path podman-compose --container-session-data-folder /tmp/devcontainers-f739ce91-e207-4b02-95c0-d7fffd1b80271776955475033 --workspace-folder /home/gdevenyi/projects/nf-neuro --workspace-mount-consistency cached --gpu-availability detect --id-label devcontainer.local_folder=/home/gdevenyi/projects/nf-neuro --id-label devcontainer.config_file=/home/gdevenyi/projects/nf-neuro/.devcontainer/devops/devcontainer.json --log-level debug --log-format json --config /home/gdevenyi/projects/nf-neuro/.devcontainer/devops/devcontainer.json --default-user-env-probe loginInteractiveShell --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root --include-configuration --include-merged-configuration
[636 ms] @devcontainers/cli 0.86.0. Node.js v22.22.1. linux 7.0.0-1-cachyos x64.
[636 ms] Start: Run: podman buildx version
[729 ms] buildah 1.43.1
[729 ms] 
[729 ms] Start: Run: podman version --format {{.Server.Version}}
[775 ms] 5.8.2
[776 ms] 
[776 ms] Start: Run: podman -v
[813 ms] Start: Resolving Remote
[819 ms] Start: Run: git rev-parse --show-cdup
[830 ms] Start: Run: podman ps -q -a --filter label=devcontainer.local_folder=/home/gdevenyi/projects/nf-neuro --filter label=devcontainer.config_file=/home/gdevenyi/projects/nf-neuro/.devcontainer/devops/devcontainer.json
[890 ms] Start: Run: podman inspect --type image python:3.13-slim-bookworm
[963 ms] Resolving Feature dependencies for 'ghcr.io/devcontainers/features/git:1'...
[964 ms] * Processing feature: ghcr.io/devcontainers/features/git:1
[967 ms] Loading 122 extra certificates from /etc/ssl/certs/ca-certificates.crt.
[1315 ms] Start: Run: docker-credential-secret get
[1985 ms] * Processing feature: ghcr.io/devcontainers/features/common-utils
[2376 ms] Resolving Feature dependencies for 'ghcr.io/devcontainers/features/github-cli:1'...
[2376 ms] * Processing feature: ghcr.io/devcontainers/features/github-cli:1
[2702 ms] * Processing feature: ghcr.io/devcontainers/features/common-utils
[3115 ms] * Processing feature: ghcr.io/devcontainers/features/git
[3432 ms] Resolving Feature dependencies for 'ghcr.io/devcontainers/features/docker-in-docker:2'...
[3432 ms] * Processing feature: ghcr.io/devcontainers/features/docker-in-docker:2
[3752 ms] * Processing feature: ghcr.io/devcontainers/features/common-utils
[4017 ms] Resolving Feature dependencies for 'ghcr.io/robsyme/features/nextflow:1'...
[4017 ms] * Processing feature: ghcr.io/robsyme/features/nextflow:1
[4597 ms] * Processing feature: ghcr.io/devcontainers/features/java
[4962 ms] Resolving Feature dependencies for 'ghcr.io/devcontainers-extra/features/tmux-apt-get:1'...
[4962 ms] * Processing feature: ghcr.io/devcontainers-extra/features/tmux-apt-get:1
[5315 ms] * Processing feature: ghcr.io/devcontainers-extra/features/apt-get-packages
[5800 ms] Soft-dependency 'ghcr.io/devcontainers/features/common-utils' is not required.  Removing from installation order...
[5800 ms] Soft-dependency 'ghcr.io/devcontainers/features/common-utils' is not required.  Removing from installation order...
[5800 ms] Soft-dependency 'ghcr.io/devcontainers/features/common-utils' is not required.  Removing from installation order...
[5800 ms] Soft-dependency 'ghcr.io/devcontainers/features/java' is not required.  Removing from installation order...
[5800 ms] Soft-dependency 'ghcr.io/devcontainers-extra/features/apt-get-packages' is not required.  Removing from installation order...
[5801 ms] * Fetching feature: tmux-apt-get_0_oci
[6230 ms] Files to omit: ''
[6253 ms] * Fetched feature: tmux-apt-get_0_oci version 1.0.17
[6253 ms] * Fetching feature: docker-in-docker_1_oci
[6707 ms] Files to omit: ''
[6714 ms] * Fetched feature: docker-in-docker_1_oci version 2.16.1
[6714 ms] * Fetching feature: git_2_oci
[7209 ms] Files to omit: ''
[7212 ms] * Fetched feature: git_2_oci version 1.3.5
[7212 ms] * Fetching feature: nextflow_3_oci
[7663 ms] Files to omit: ''
[7666 ms] * Fetched feature: nextflow_3_oci version 1.2.0
[7667 ms] * Fetching feature: github-cli_4_oci
[8137 ms] Files to omit: ''
[8149 ms] * Fetched feature: github-cli_4_oci version 1.1.0
[8155 ms] Start: Run: getenforce 
[8174 ms] Start: Run: podman buildx build --load --build-arg BUILDKIT_INLINE_CACHE=1 -f /tmp/devcontainercli-gdevenyi/container-features/0.86.0-1776955477110/Dockerfile-with-features -t vsc-nf-neuro-ab146082f32e237fd43e784dfc924e9eb65e819d2e909c9bcc31c0594a127615 --target dev_containers_target_stage --build-arg NFTEST_VERSION=0.9.3 --build-arg POETRY_VERSION=2.* --build-arg NFT_DIFF=pdiff --build-arg NFT_DIFF_ARGS=--line-numbers --width 120 --expand-tabs=2 --build-context dev_containers_feature_content_source=/tmp/devcontainercli-gdevenyi/container-features/0.86.0-1776955477110 --build-arg _DEV_CONTAINERS_BASE_IMAGE=dev_container_auto_added_stage_label --build-arg _DEV_CONTAINERS_IMAGE_USER=neuro --build-arg _DEV_CONTAINERS_FEATURE_CONTENT_SOURCE=dev_container_feature_content_temp /home/gdevenyi/projects/nf-neuro/.devcontainer/devops
[1/3] STEP 1/18: FROM python:3.13-slim-bookworm AS dev_container_auto_added_stage_label
[1/3] STEP 2/18: ARG NFTEST_VERSION
--> Using cache 4f5e6f053fc2db7906afa95d168e0df0573791f220779559cca0a05aa0296bd8
--> 4f5e6f053fc2
[1/3] STEP 3/18: ARG POETRY_VERSION
--> Using cache 90d63d2db2043b01c31dc90df46f2f065ad94ac1446a467f1df31ccb778b4847
--> 90d63d2db204
[1/3] STEP 4/18: ARG USERNAME=neuro
--> Using cache 369780f5692ca44b406c1d14b4bf21630c80cdc6596edaea3929f1d1a13f0365
--> 369780f5692c
[1/3] STEP 5/18: ARG USER_UID=1000
--> Using cache 770753d95a31fefaafa8d2f49a15b31c806a40eacc3fa247b2ba4d8be6c6daf5
--> 770753d95a31
[1/3] STEP 6/18: ARG USER_GID=$USER_UID
--> Using cache 9fc531fd1e4eb0508edc4254b403463ac15cfc0f17bb8d0c0f6534a61d6837a8
--> 9fc531fd1e4e
[1/3] STEP 7/18: ENV NODE_MAJOR=20
--> Using cache 7af116733832ea6d04fee17aead203642462162b1e76118d3562e5b20cd99a5f
--> 7af116733832
[1/3] STEP 8/18: ENV ACTIONLINT_VERSION=1.7.7
--> Using cache 73059f18113397d2529fdf813162c88d5b0126da1e9a7557c4d3f1ac3c7dd666
--> 73059f181133
[1/3] STEP 9/18: ENV NFTEST_VERSION=${NFTEST_VERSION:-0.9.3}
--> Using cache bf4dc852f339f17f92bf8fcf1c9c8f00da46f937a04bd19f704c438eea4a7052
--> bf4dc852f339
[1/3] STEP 10/18: ENV POETRY_VERSION=${POETRY_VERSION:-2.*}
--> Using cache 37dd1dca232b7b32ff262f141af9a1dce30dc02456d2421c356a01ecf8413e75
--> 37dd1dca232b
[1/3] STEP 11/18: RUN apt update && apt install -y         curl         git         jq         openjdk-17-jre         pipx         sudo         wget     && rm -rf /var/lib/apt/lists/*
--> Using cache 139321aa92d165586fa6989e86b4db49e13caab6bf87a760c416240042a96357
--> 139321aa92d1
[1/3] STEP 12/18: RUN curl -fsSL https://raw.githubusercontent.com/nektos/act/master/install.sh | bash &&     curl -fsSL https://github.com/rhysd/actionlint/releases/download/v${ACTIONLINT_VERSION}/actionlint_${ACTIONLINT_VERSION}_linux_amd64.tar.gz |     tar xz -C /usr/local/bin actionlint &&     chmod +x /usr/local/bin/actionlint
--> Using cache b62acfb2de477f87b9f381fd3dc96bbbc379f94efb60c1c450bbc1c98177ddfb
--> b62acfb2de47
[1/3] STEP 13/18: RUN curl -fsSL https://deb.nodesource.com/setup_${NODE_MAJOR}.x | bash - &&    apt-get install -y nodejs &&     groupadd --gid 501 yeoman &&     groupadd --gid 1010 nodeusers &&     useradd --uid 501 --gid yeoman --shell /bin/bash --create-home yeoman &&     echo "yeoman ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers &&     mkdir /generated &&     chown yeoman:yeoman /generated &&     mkdir -p -m 0775 /usr/local/lib/node_modules &&     chown -R root:nodeusers /usr/local/lib/node_modules
--> Using cache de1911d712fc06e0b2b87ce9ff39c2d935500c01ee8341ae64c95f838ffc0225
--> de1911d712fc
[1/3] STEP 14/18: RUN groupadd --gid $USER_GID $USERNAME &&     useradd --uid $USER_UID --gid $USER_GID -m $USERNAME &&     usermod -s /bin/bash -aG nodeusers $USERNAME &&     echo $USERNAME ALL=\(root\) NOPASSWD:ALL > /etc/sudoers.d/$USERNAME &&     chmod 0440 /etc/sudoers.d/$USERNAME &&     echo "prefix=/usr/local" >> /home/$USERNAME/.npmrc
--> Using cache 5d3518f8e5f192933371cd01b1aa929577e223b593f09fd6bfa1782d84e5e729
--> 5d3518f8e5f1
[1/3] STEP 15/18: USER $USERNAME
--> Using cache cec2ecc0f3beecfd15f518f0fa75a9b7e5de393b0fb7eb4a46f12c9066042246
--> cec2ecc0f3be
[1/3] STEP 16/18: RUN pipx ensurepath &&     pipx install poetry==${POETRY_VERSION}
--> Using cache 4142b9219bf78be867ffdcc99e2c86cb0e36a3105da1f0197bfe879f83e35c88
--> 4142b9219bf7
[1/3] STEP 17/18: RUN SNIPPET="export PROMPT_COMMAND='history -a' && export HISTFILE=/home/$USERNAME/commandhistory/.bash_history"     && echo "$SNIPPET" >> "/home/$USERNAME/.bashrc"
--> Using cache ff756175edd3266f9cd023151f4a6c96d5e1334080e05ae6f881f0ebc2b78180
--> ff756175edd3
[1/3] STEP 18/18: ENTRYPOINT ["/bin/sh", "-lc", "pipx ensurepath && exec \"$@\""]
--> Using cache e9c26746dd1c0ead05c2d7e5810ee8ba53fb1171dbbd70d3571284c65af00311
--> e9c26746dd1c
[2/3] STEP 1/4: FROM e9c26746dd1c0ead05c2d7e5810ee8ba53fb1171dbbd70d3571284c65af00311 AS dev_containers_feature_content_normalize
[2/3] STEP 2/4: USER root
--> Using cache 35c68c06a2c417c8c33bcb6fe601182a253e2d914055e5d5ec185a58ccbe7b57
--> 35c68c06a2c4
[2/3] STEP 3/4: COPY --from=dev_containers_feature_content_source devcontainer-features.builtin.env /tmp/build-features/
--> Using cache a1e815e509fd15c735bc6fec6b954185beadd0f78de8cd9198aa7e5be8ddd54b
--> a1e815e509fd
[2/3] STEP 4/4: RUN chmod -R 0755 /tmp/build-features/
--> Using cache eba16bcbeb3db1e685ba613aa3009cf13c3511e3581ef068f852ed7a696073e9
--> eba16bcbeb3d
[3/3] STEP 1/15: FROM e9c26746dd1c0ead05c2d7e5810ee8ba53fb1171dbbd70d3571284c65af00311 AS dev_containers_target_stage
[3/3] STEP 2/15: USER root
--> Using cache 35c68c06a2c417c8c33bcb6fe601182a253e2d914055e5d5ec185a58ccbe7b57
--> 35c68c06a2c4
[3/3] STEP 3/15: RUN mkdir -p /tmp/dev-container-features
--> Using cache 3f32d050b5835bf7ef9f1b1c3851092e5db5a36df4b4e1a504f3c376431b8a45
--> 3f32d050b583
[3/3] STEP 4/15: COPY --from=dev_containers_feature_content_normalize /tmp/build-features/ /tmp/dev-container-features
--> Using cache d6be9ec72c3a6846a7a3d2db4689be94b30a79b557681dc0952eda69a2fed4cc
--> d6be9ec72c3a
[3/3] STEP 5/15: RUN echo "_CONTAINER_USER_HOME=$( (command -v getent >/dev/null 2>&1 && getent passwd 'neuro' || grep -E '^neuro|^[^:]*:[^:]*:neuro:' /etc/passwd || true) | cut -d: -f6)" >> /tmp/dev-container-features/devcontainer-features.builtin.env && echo "_REMOTE_USER_HOME=$( (command -v getent >/dev/null 2>&1 && getent passwd 'neuro' || grep -E '^neuro|^[^:]*:[^:]*:neuro:' /etc/passwd || true) | cut -d: -f6)" >> /tmp/dev-container-features/devcontainer-features.builtin.env
--> Using cache ffbd5685149fa82febfc470cc72f136b2e8d02f5e8218c8476e928bc692f237e
--> ffbd5685149f
[3/3] STEP 6/15: RUN --mount=type=bind,from=dev_containers_feature_content_source,source=tmux-apt-get_0,target=/tmp/build-features-src/tmux-apt-get_0     cp -ar /tmp/build-features-src/tmux-apt-get_0 /tmp/dev-container-features  && chmod -R 0755 /tmp/dev-container-features/tmux-apt-get_0  && cd /tmp/dev-container-features/tmux-apt-get_0  && chmod +x ./devcontainer-features-install.sh  && ./devcontainer-features-install.sh  && rm -rf /tmp/dev-container-features/tmux-apt-get_0
--> Using cache f930933fec325db1a8bd8b24615d190f453e504b205fb60428a612290167571e
--> f930933fec32
[3/3] STEP 7/15: ENV DOCKER_BUILDKIT="1"
--> Using cache 6003f8d85f4656358741ea5dd86eee7d09ddc650b27cee910a5350c37d76f591
--> 6003f8d85f46
[3/3] STEP 8/15: RUN --mount=type=bind,from=dev_containers_feature_content_source,source=docker-in-docker_1,target=/tmp/build-features-src/docker-in-docker_1     cp -ar /tmp/build-features-src/docker-in-docker_1 /tmp/dev-container-features  && chmod -R 0755 /tmp/dev-container-features/docker-in-docker_1  && cd /tmp/dev-container-features/docker-in-docker_1  && chmod +x ./devcontainer-features-install.sh  && ./devcontainer-features-install.sh  && rm -rf /tmp/dev-container-features/docker-in-docker_1
--> Using cache aace6a3af3d796ea0a93ef44a9d40f8fb3826f84b69e221581f70789894d9a72
--> aace6a3af3d7
[3/3] STEP 9/15: RUN --mount=type=bind,from=dev_containers_feature_content_source,source=git_2,target=/tmp/build-features-src/git_2     cp -ar /tmp/build-features-src/git_2 /tmp/dev-container-features  && chmod -R 0755 /tmp/dev-container-features/git_2  && cd /tmp/dev-container-features/git_2  && chmod +x ./devcontainer-features-install.sh  && ./devcontainer-features-install.sh  && rm -rf /tmp/dev-container-features/git_2
--> Using cache c4bc5fe21a5f83fa2035fa1402cc5982218a11508ef42030e49e16cda7f5e1f2
--> c4bc5fe21a5f
[3/3] STEP 10/15: RUN --mount=type=bind,from=dev_containers_feature_content_source,source=nextflow_3,target=/tmp/build-features-src/nextflow_3     cp -ar /tmp/build-features-src/nextflow_3 /tmp/dev-container-features  && chmod -R 0755 /tmp/dev-container-features/nextflow_3  && cd /tmp/dev-container-features/nextflow_3  && chmod +x ./devcontainer-features-install.sh  && ./devcontainer-features-install.sh  && rm -rf /tmp/dev-container-features/nextflow_3
===========================================================================
Feature       : Nextflow
Description   : Nextflow feature
Id            : ghcr.io/robsyme/features/nextflow
Version       : 1.2.0
Documentation : 
Options       :

===========================================================================
+ USERNAME=neuro
+ NEXTFLOW_DIR=/usr/local/bin
++ id -u
+ '[' 0 -ne 0 ']'
+ '[' neuro = auto ']'
+ '[' neuro = automatic ']'
+ '[' neuro = none ']'
+ id -u neuro
+ cat /etc/group
+ grep -e '^nextflow:'
+ groupadd -r nextflow
+ check_packages curl ca-certificates zip unzip sed default-jdk
+ dpkg -s curl ca-certificates zip unzip sed default-jdk
+ apt_get_update
++ find '/var/lib/apt/lists/*'
++ wc -l
find: '/var/lib/apt/lists/*': No such file or directory
+ '[' 0 = 0 ']'
+ echo 'Running apt-get update...'
Running apt-get update...
+ apt-get update -y
Get:1 http://deb.debian.org/debian bookworm InRelease [151 kB]
Get:2 http://deb.debian.org/debian bookworm-updates InRelease [55.4 kB]
Err:1 http://deb.debian.org/debian bookworm InRelease
  Couldn't create temporary file /tmp/apt.conf.2MT8An for passing config to apt-key
Err:2 http://deb.debian.org/debian bookworm-updates InRelease
  Couldn't create temporary file /tmp/apt.conf.itOX72 for passing config to apt-key
Get:3 http://deb.debian.org/debian-security bookworm-security InRelease [48.0 kB]
Err:3 http://deb.debian.org/debian-security bookworm-security InRelease
  Couldn't create temporary file /tmp/apt.conf.WChjjD for passing config to apt-key
Get:4 https://deb.nodesource.com/node_20.x nodistro InRelease [12.1 kB]
Err:4 https://deb.nodesource.com/node_20.x nodistro InRelease
  Couldn't create temporary file /tmp/apt.conf.fbdNQ7 for passing config to apt-key
Get:5 https://packages.microsoft.com/repos/microsoft-debian-bookworm-prod bookworm InRelease [3618 B]
Err:5 https://packages.microsoft.com/repos/microsoft-debian-bookworm-prod bookworm InRelease
  Couldn't create temporary file /tmp/apt.conf.C0dnwp for passing config to apt-key
Reading package lists...
W: GPG error: http://deb.debian.org/debian bookworm InRelease: Couldn't create temporary file /tmp/apt.conf.2MT8An for passing config to apt-key
E: The repository 'http://deb.debian.org/debian bookworm InRelease' is not signed.
W: GPG error: http://deb.debian.org/debian bookworm-updates InRelease: Couldn't create temporary file /tmp/apt.conf.itOX72 for passing config to apt-key
E: The repository 'http://deb.debian.org/debian bookworm-updates InRelease' is not signed.
W: GPG error: http://deb.debian.org/debian-security bookworm-security InRelease: Couldn't create temporary file /tmp/apt.conf.WChjjD for passing config to apt-key
E: The repository 'http://deb.debian.org/debian-security bookworm-security InRelease' is not signed.
W: GPG error: https://deb.nodesource.com/node_20.x nodistro InRelease: Couldn't create temporary file /tmp/apt.conf.fbdNQ7 for passing config to apt-key
E: The repository 'https://deb.nodesource.com/node_20.x nodistro InRelease' is not signed.
W: GPG error: https://packages.microsoft.com/repos/microsoft-debian-bookworm-prod bookworm InRelease: Couldn't create temporary file /tmp/apt.conf.C0dnwp for passing config to apt-key
E: The repository 'https://packages.microsoft.com/repos/microsoft-debian-bookworm-prod bookworm InRelease' is not signed.
ERROR: Feature "Nextflow" (ghcr.io/robsyme/features/nextflow) failed to install!
Error: building at STEP "RUN --mount=type=bind,from=dev_containers_feature_content_source,source=nextflow_3,target=/tmp/build-features-src/nextflow_3 cp -ar /tmp/build-features-src/nextflow_3 /tmp/dev-container-features  && chmod -R 0755 /tmp/dev-container-features/nextflow_3  && cd /tmp/dev-container-features/nextflow_3  && chmod +x ./devcontainer-features-install.sh  && ./devcontainer-features-install.sh  && rm -rf /tmp/dev-container-features/nextflow_3": while running runtime: exit status 100
[10891 ms] Error: Command failed: podman buildx build --load --build-arg BUILDKIT_INLINE_CACHE=1 -f /tmp/devcontainercli-gdevenyi/container-features/0.86.0-1776955477110/Dockerfile-with-features -t vsc-nf-neuro-ab146082f32e237fd43e784dfc924e9eb65e819d2e909c9bcc31c0594a127615 --target dev_containers_target_stage --build-arg NFTEST_VERSION=0.9.3 --build-arg POETRY_VERSION=2.* --build-arg NFT_DIFF=pdiff --build-arg NFT_DIFF_ARGS=--line-numbers --width 120 --expand-tabs=2 --build-context dev_containers_feature_content_source=/tmp/devcontainercli-gdevenyi/container-features/0.86.0-1776955477110 --build-arg _DEV_CONTAINERS_BASE_IMAGE=dev_container_auto_added_stage_label --build-arg _DEV_CONTAINERS_IMAGE_USER=neuro --build-arg _DEV_CONTAINERS_FEATURE_CONTENT_SOURCE=dev_container_feature_content_temp /home/gdevenyi/projects/nf-neuro/.devcontainer/devops
[10891 ms]     at GV (/home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js:466:2009)
[10891 ms]     at async Rp (/home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js:465:1910)
[10892 ms]     at async uG (/home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js:465:608)
[10892 ms]     at async ZV (/home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js:483:4649)
[10892 ms]     at async kI (/home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js:483:5768)
[10892 ms]     at async MZ (/home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js:664:205)
[10892 ms]     at async kZ (/home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js:663:15080)
[10892 ms]     at async /home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js:483:1917
[10899 ms] Exit code 1
[10908 ms] Command failed: /opt/visual-studio-code/code /home/gdevenyi/.vscode/extensions/ms-vscode-remote.remote-containers-0.454.0/dist/spec-node/devContainersSpecCLI.js up --user-data-folder /home/gdevenyi/.config/Code/User/globalStorage/ms-vscode-remote.remote-containers/data --docker-path podman --docker-compose-path podman-compose --container-session-data-folder /tmp/devcontainers-f739ce91-e207-4b02-95c0-d7fffd1b80271776955475033 --workspace-folder /home/gdevenyi/projects/nf-neuro --workspace-mount-consistency cached --gpu-availability detect --id-label devcontainer.local_folder=/home/gdevenyi/projects/nf-neuro --id-label devcontainer.config_file=/home/gdevenyi/projects/nf-neuro/.devcontainer/devops/devcontainer.json --log-level debug --log-format json --config /home/gdevenyi/projects/nf-neuro/.devcontainer/devops/devcontainer.json --default-user-env-probe loginInteractiveShell --mount type=volume,source=vscode,target=/vscode,external=true --skip-post-create --update-remote-user-uid-default on --mount-workspace-git-root --include-configuration --include-merged-configuration
[10908 ms] Exit code 1

[arnaudbore]

I can't reproduce ☹️ - I just tried and didn't have any issue, maybe a temporary issue ?

[gdevenyi]

Its probably my network's fault.

Is it possible to make the devcontainer stuff available as pullable from ghcr or docker? Building it locally is very difficult with my network issues.

[arnaudbore]

The truth, even tho I don't have any issue with my network I'm now coding everything without the need for this devcontainer.
All you need is nf-core and nf-test which are very easy to install.
Having said that, I'll talk to Alex and see if we have some time to offer a second solution.

[gagnonanthony]

I was about to say, you don't technically need the container. Installing nf-core, nf-test, and nextflow should be sufficient and might be easier if you encounter network issues.

[gdevenyi]

Installing nf-core, nf-test, and nextflow

OK cool. Is there a virtualenvironment style one-shot to do this?

[AlexVCaron]

Hi @gdevenyi. I just realized looking at the logs you are using podman. Again in the logs, I see that the errors appear when building devcontainer features atop the image definition, related to permissions on TMPDIR. Turns out, it is a known limitation of podman's builder buildah (more here also).

[AlexVCaron]

I can look into distributing an all-in-one container with everything in it, but assume the problem will get resolved on podman's side eventually. For the time being, it's maybe more straightforward to go the local installation route.

[gdevenyi]

go the local installation route.

Is there a one-shot local install command.

[AlexVCaron]

We need to add back manual installation to the documentation. It was removed in favor of the devcontainer, from which everyone except me seem to have fallen of ... Anyway, for the time being, here's a procedure that should get you there.

1. First, validate you have java and npm installed. The installation procedure is really specific to your machine setup, so you need to find how to setup this correctly. I can give some tips if needed, but wont give a full walkthrough for this.

2. Run these in the repo root, they should get your environment up and running :

mkdir -p $HOME/.local/bin/
curl -s https://get.nextflow.io | bash
chmod +x nextflow
mv nextflow $HOME/.local/bin/
curl -fsSL https://get.nf-test.com | bash
chmod +x nf-test
mv nf-test $HOME/.local/bin/
curl -sSL https://install.python-poetry.org | python3 -
poetry install --no-root
npm install -g --save-dev --save-exact prettier
npm install -g --save-dev editorconfig
npm install -g --save-dev editorconfig-checker

3. Setup the CLI environment like for the devcontainer. Considering your nf-neuro clone doesn't change, also setup those variables in your .bashrc :

NFCORE_MODULES_GIT_REMOTE=<url to your fork>
NFCORE_MODULES_BRANCH=<main branch of your fork>
NFCORE_SUBWORKFLOWS_GIT_REMOTE=<url to your fork>
NFCORE_SUBWORKFLOWS_BRANCH=<main branch of your fork>

4. Also, since you use podman instead of docker, it would be worthwhile trying to setup nf-test against it. Also add this in the .bashrc :

PROFILE=podman

[gdevenyi]

I think this really needs a pixi/uv or somesuch virtualenvironment setup. I absolutely hate polluting my global profile

[AlexVCaron]

I agree on this. We already use poetry for python dependencies. I forgot to specify, it will create an environment for the project (centralized in /usr/.local I think). For the rest, I don't really know of any environment setup for Java and Node. If you have any experience with that, it would be a nice contribution !

I absolutely hate polluting my global profile