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Fix -dockerized execution #3137 #3148

Merged
merged 8 commits into from
Nov 2, 2022
Merged

Fix -dockerized execution #3137 #3148

merged 8 commits into from
Nov 2, 2022

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Kibubu
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@Kibubu Kibubu commented Aug 24, 2022

Fix dockerize execution #3137

Amazon's Corretto docker image is missing basic user management utilities the entry script relies on.

Added utilities to Dockerfile
Fixed execution of nextflow within docker Container

Squash

The utilities adduser and addgroup are not installed inside the container image

Changed to useradd and groupadd added their dependencies to Dockerfile

Fix could not create plugins folder

The permissions of /.nextflow were to restricted to

Fix Typo and move comments to correct location


Test script

#! /bin/bash

git clone  git@github.com:kibubu/nextflow.git fix-dockerize
cd fix-dockerize/docker || exit
git checkout Fix-dockerize
curl -s https://get.nextflow.io | bash
mkdir -p dist/linux/amd64
cp "$(which docker)" dist/linux/amd64
docker rmi nextflow/nextflow:22.04.5
docker build . -t nextflow/nextflow:22.04.5
mkdir tmp && cd tmp || exit
../nextflow -dockerize run nextflow-io/hello
sleep 5
which tree || exit
tree -a .
cd ..

asciicast

Kibubu and others added 8 commits August 24, 2022 14:31
The utilities adduser and addgroup are not part of the used
container image

Changed to useradd and groupadd anded their dependencies to Dockerfile

Fix could not create plugins folder

The permissions of /.nextflow were to restricted to

Fix Typo and move comments to correct location

Signed-off-by: Kirill Bulert <bulert@infai.org>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Kirill Bulert <bulert@infai.org>
Signed-off-by: Mike Lee <michael.lee0517@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Kirill Bulert <bulert@infai.org>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Kirill Bulert <bulert@infai.org>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Kirill Bulert <bulert@infai.org>
Signed-off-by: Kirill Bulert <bulert@infai.org>
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: Kirill Bulert <bulert@infai.org>
@Kibubu Kibubu closed this by deleting the head repository Aug 31, 2022
@Kibubu
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Kibubu commented Aug 31, 2022

I messed, totally forget that this PR was still open and deleted my fork, since I was to lazy to resolve merge conflicts.

Let's see what happens if I press reopen

...seriously embarrassed right now

@pditommaso pditommaso merged commit 64a81a5 into nextflow-io:master Nov 2, 2022
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Thanks for this contribution

@bentsherman bentsherman linked an issue Feb 2, 2023 that may be closed by this pull request
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Container issues in the docker driven execution (-dockerize)
4 participants