63 lines
1.9 KiB
Bash
Executable File
63 lines
1.9 KiB
Bash
Executable File
#!/bin/bash
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#
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# Copyright 2013-2026, Seqera Labs
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#
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# Licensed under the Apache License, Version 2.0 (the "License");
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# you may not use this file except in compliance with the License.
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# You may obtain a copy of the License at
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#
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# http://www.apache.org/licenses/LICENSE-2.0
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#
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# Unless required by applicable law or agreed to in writing, software
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# distributed under the License is distributed on an "AS IS" BASIS,
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# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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# See the License for the specific language governing permissions and
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# limitations under the License.
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#
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#
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# This script acts as a pass-through container entry point. Its main role
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# is to create a user able to execute docker commands from the container
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# connecting to the host docker socket at runtime.
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#
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# The invoker needs to pass the user ID using the variable NXF_USRMAP.
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# When this variable is defined, it creates a new user in the container
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# with such ID and adds it to the `docker` group, then assigns the docker
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# socket file ownership to that user.
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#
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# Finally it switches the `nextflow` user using the `su` command and
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# executes the original target command line.
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#
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# authors:
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# Paolo Di Tommaso
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# Emilio Palumbo
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#
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# enable debugging
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[[ "$NXF_DEBUG_ENTRY" ]] && set -x
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# wrap cli args with single quote to avoid wildcard expansion
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cli=''; for x in "$@"; do cli+="'$x' "; done
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# the NXF_USRMAP hold the user ID in the host environment
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if [[ "$NXF_USRMAP" ]]; then
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# create a `nextflow` user with the provided ID
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groupadd docker
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useradd -u "$NXF_USRMAP" -G docker -s /bin/bash nextflow
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# then change the docker socket ownership to `nextflow` user
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# and change the $NXF_HOME ownership to `nextflow` user
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chown nextflow /var/run/docker.sock
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chown -R nextflow /.nextflow
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# finally run the target command with `nextflow` user
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su nextflow << EOF
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[[ "$NXF_DEBUG_ENTRY" ]] && set -x
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exec bash -c "$cli"
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EOF
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# otherwise just execute the command
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else
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exec bash -c "$cli"
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fi
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