add nextflow d30e48d

nextflow/docker/Dockerfile

@@ -0,0 +1,19 @@
+FROM amazoncorretto:21-al2023
+RUN yum install -y procps-ng shadow-utils which
+
+ENV NXF_HOME=/.nextflow
+ARG TARGETPLATFORM=linux/amd64
+
+# copy docker client
+COPY dist/${TARGETPLATFORM}/docker /usr/local/bin/docker
+COPY entry.sh /usr/local/bin/entry.sh
+COPY nextflow /usr/local/bin/nextflow
+
+# download runtime
+RUN mkdir /.nextflow \
+ && chmod 755 /usr/local/bin/nextflow \
+ && chmod 755 /usr/local/bin/entry.sh \
+ && nextflow info
+
+# define the entry point
+ENTRYPOINT ["/usr/local/bin/entry.sh"]

nextflow/docker/Makefile

@@ -0,0 +1,45 @@
+#
+#  Copyright 2013-2024, Seqera Labs
+#
+#  Licensed under the Apache License, Version 2.0 (the "License");
+#  you may not use this file except in compliance with the License.
+#  You may obtain a copy of the License at
+#
+#      http://www.apache.org/licenses/LICENSE-2.0
+#
+#  Unless required by applicable law or agreed to in writing, software
+#  distributed under the License is distributed on an "AS IS" BASIS,
+#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+#  See the License for the specific language governing permissions and
+#  limitations under the License.
+
+version ?= none
+
+build: dist/docker/amd64
+	cp ../nextflow .
+	docker buildx build --platform linux/amd64 --output=type=docker --progress=plain --tag nextflow/nextflow:${version} --build-arg TARGETPLATFORM=linux/amd64 .
+
+build-arm: dist/docker/arm64
+	cp ../nextflow .
+	docker buildx build --platform linux/arm64 --output=type=docker --progress=plain --tag nextflow/nextflow:${version} --build-arg TARGETPLATFORM=linux/arm64 .
+
+release: build
+	docker push nextflow/nextflow:${version}
+	#
+	docker tag nextflow/nextflow:${version} public.cr.seqera.io/nextflow/nextflow:${version}
+	docker push public.cr.seqera.io/nextflow/nextflow:${version}
+
+#Static builds can now be found at:
+#
+#  Linux:   https://download.docker.com/linux/static
+#  MacOS:   https://download.docker.com/mac/static
+#  Windows: https://download.docker.com/win/static
+
+dist/docker/amd64:
+	mkdir -p dist/linux/amd64
+	curl -fsSL https://download.docker.com/linux/static/stable/x86_64/docker-19.03.15.tgz | tar --strip-components=1 -xvz -C dist/linux/amd64
+
+dist/docker/arm64:
+	mkdir -p dist/linux/arm64
+	curl -fsSL https://download.docker.com/linux/static/stable/aarch64/docker-19.03.15.tgz | tar --strip-components=1 -xvz -C dist/linux/arm64
+

nextflow/docker/entry.sh

@@ -0,0 +1,62 @@
+#!/bin/bash
+#
+# Copyright 2013-2026, Seqera Labs
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+
+#
+# This script acts as a pass-through container entry point. Its main role
+# is to create a user able to execute docker commands from the container
+# connecting to the host docker socket at runtime.
+#
+# The invoker needs to pass the user ID using the variable NXF_USRMAP.
+# When this variable is defined, it creates a new user in the container
+# with such ID and adds it to the `docker` group, then assigns the docker
+# socket file ownership to that user.
+#
+# Finally it switches the `nextflow` user using the `su` command and
+# executes the original target command line.
+#
+# authors:
+#  Paolo Di Tommaso
+#  Emilio Palumbo
+#
+
+# enable debugging
+[[ "$NXF_DEBUG_ENTRY" ]] && set -x
+
+# wrap cli args with single quote to avoid wildcard expansion
+cli=''; for x in "$@"; do cli+="'$x' "; done
+
+# the NXF_USRMAP hold the user ID in the host environment
+if [[ "$NXF_USRMAP" ]]; then
+# create a `nextflow` user with the provided ID
+groupadd docker
+useradd -u "$NXF_USRMAP" -G docker -s /bin/bash nextflow
+
+# then change the docker socket ownership to `nextflow` user
+# and change the $NXF_HOME ownership to `nextflow` user
+chown nextflow /var/run/docker.sock
+chown -R nextflow /.nextflow
+
+# finally run the target command with `nextflow` user
+su nextflow << EOF
+[[ "$NXF_DEBUG_ENTRY" ]] && set -x
+exec bash -c "$cli"
+EOF
+
+# otherwise just execute the command
+else
+exec bash -c "$cli"
+fi

nextflow/docker/flux/README.md

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+# Flux Container Environment
+
+In this directory we include a [Dockerfile](.devcontainer/Dockerfile)
+along with a [VSCode Developer Container](https://code.visualstudio.com/docs/devcontainers/containers) 
+environment that you can put at the root of the project to be provided with a Flux agent and the dependencies
+needed to build Nextflow. See the [documentation](https://www.nextflow.io/docs/latest/flux.html) 
+for the latest for how to use them.
+