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running container without args shouldnt be error return code
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‎.circleci/config.yml‎

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# This is a continuous build CircleCI configuration for a Docker container
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# intended to bulid on CircleCI to spread out testing over Travis/Circle.
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# The container is built and pushed to the CONTAINER_NAME variable
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# defined here or within the CircleCI settings. The following environment
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# variables are acceptable here or in these settings (for sensitive information)
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#
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# CONTAINER_NAME
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# DOCKER_USER
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# DOCKER_EMAIL
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################################################################################
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# Functions
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################################################################################
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# Defaults
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defaults: &defaults
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docker:
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- image: docker:18.01.0-ce-git
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working_directory: /tmp/src
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environment:
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- CONTAINER_NAME: singularityware/docker2singularity
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# Installation
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install: &install
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name: Install parallel gzip, gettext, python3, and jq
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command: apk add --no-cache pigz python3 gettext jq
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dockerload: &dockerload
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name: Load Docker container Image
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no_output_timeout: 30m
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command: |
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echo "Working directory is ${PWD}"
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docker info
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set +o pipefail
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if [ -f /tmp/cache/container.tar.gz ]; then
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apk update && apk add --no-cache pigz curl curl-dev
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pigz -d --stdout /tmp/cache/container.tar.gz | docker load
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fi
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dockersave: &dockersave
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name: Docker Save
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no_output_timeout: 40m
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command: |
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DOCKER_TAG="v$(cat VERSION)"
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echo "Saving ${CONTAINER_NAME}:${DOCKER_TAG} to container.tar.gz"
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mkdir -p /tmp/cache
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docker save ${CONTAINER_NAME}:${DOCKER_TAG} \
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| pigz -2 -p 3 > /tmp/cache/container.tar.gz
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dockerdeploy: &dockerdeploy
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name: Deploy to Docker Hub
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no_output_timeout: 40m
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command: |
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docker images
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DOCKER_TAG="v$(cat VERSION)"
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echo "Container name set to ${CONTAINER_NAME}:${DOCKER_TAG}"
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if [[ -n "$DOCKER_PASS" ]]; then
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docker login -u $DOCKER_USER -p $DOCKER_PASS
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docker push ${CONTAINER_NAME}:${DOCKER_TAG}
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echo "Tagging latest image..."
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docker tag ${CONTAINER_NAME}:${DOCKER_TAG} ${CONTAINER_NAME}:latest
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docker push ${CONTAINER_NAME}:latest
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fi
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dockerbuild: &dockerbuild
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name: Build development Docker container
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command: |
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echo "Building base image..."
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DOCKER_TAG="v$(cat VERSION)"
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docker build -t ${CONTAINER_NAME}:${DOCKER_TAG} .
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################################################################################
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# Jobs
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################################################################################
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version: 2
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jobs:
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build:
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<<: *defaults
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steps:
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- checkout
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- restore_cache:
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keys:
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- docker-v1-{{ .Branch }}
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paths:
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- /tmp/cache/container.tar.gz
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- restore_cache:
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key: dependency-cache
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- setup_remote_docker
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- run: *install
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- run: *dockerload
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- run: *dockerbuild
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- run: *dockersave
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- persist_to_workspace:
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root: /tmp
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paths:
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- src
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- cache
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update_cache:
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<<: *defaults
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steps:
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- attach_workspace:
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at: /tmp
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- save_cache:
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key: docker-v1-{{ .Branch }}
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paths:
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- /tmp/cache/container.tar.gz
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deploy:
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<<: *defaults
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steps:
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- attach_workspace:
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at: /tmp
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- setup_remote_docker
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- run: *dockerload
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- run: *dockerdeploy
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################################################################################
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# Workflows
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################################################################################
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workflows:
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version: 2
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build_deploy:
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jobs:
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- build:
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filters:
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branches:
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ignore:
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- gh-pages
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- /docs?/.*/
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tags:
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only: /.*/
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- update_cache:
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requires:
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- build
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filters:
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branches:
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ignore:
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- gh-pages
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- /docs?/.*/
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tags:
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only: /.*/
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# Upload the container to Docker Hub
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- deploy:
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requires:
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- build
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- update_cache
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filters:
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branches:
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only: master
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tags:
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only: /.*/

‎AUTHORS.md‎

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## Maintainers
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- [@chrisfilo](https://www.github.com/chrisfilo)
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- [@vsoch](https://www.github.com/vsoch)
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## Contributors
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- [@pvanheus](https://www.github.com/pvanheus)
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- [@kaczmarj](https://www.github.com/kaczmarj)
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- [@alanhoyle](https://www.github.com/alanhoyle)
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- [@justbennet](https://www.github.com/justbennet)
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- [@pditommaso](https://www.github.com/pditommaso)
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- [@jdidion](https://www.github.com/jdidion)
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- [@alaindomissy](https://www.github.com/alaindomissy)

‎CHANGELOG.md‎

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@@ -13,7 +13,9 @@ represented by the pull requests that fixed them. Critical items to know are:
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- changed behaviour (recipe sections work differently)
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This changelog was started with version of Singularity v2.5, and reflects changes since then.
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The tags here reflect tags on Docker Hub
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## [master](https://github.com/singularityware/docker2singularity/tree/master) (master)
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- update of Singularity from [v2.5](https://github.com/singularityware/docker2singularity/tree/v2.5) to [v2.6](https://github.com/singularityware/docker2singularity/tree/v2.6), including adding libarchive dependency, and custom name with -n (v2.6)
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- update of Singularity from [v2.4](https://github.com/singularityware/docker2singularity/tree/v2.4) to [v2.5](https://github.com/singularityware/docker2singularity/tree/v2.5), including adding libarchive dependency, and custom name with -n (v2.5)
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- addition of automated builds via CircleCI, and Authors.md (v2.5)
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- update of Singularity from [v2.4](https://github.com/singularityware/docker2singularity/tree/v2.4) to [v2.5](https://github.com/singularityware/docker2singularity/tree/v2.5), including adding libarchive dependency, and custom name with -n

‎README.md‎

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# `docker2singularity`
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Are you developing Docker images and you would like to run them on an HPC cluster supporting [Singularity](http://singularity.lbl.gov)? Are you working on Mac or Windows with no easy access to a Linux machine? If the pull, import, and general commands to [work with docker images provided by Singularity](http://singularity.lbl.gov/docs-docker) natively do not fit your needs, `docker2singularity` is an alternative way to generate Singularity images. This particular branch is intended for Singularity 2.4, which gives you a selection of image formats to build.
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<img src="https://camo.githubusercontent.com/49f33b2464042e323b43dfb587323f80d2329840/68747470733a2f2f7777772e73796c6162732e696f2f6775696465732f322e352e312f757365722d67756964652f5f7374617469632f6c6f676f2e706e67" alt="https://www.sylabs.io/guides/2.5.1/user-guide/_static/logo.png" data-canonical-src="https://www.sylabs.io/guides/2.5.1/user-guide/_static/logo.png" width="200" height="200">
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[![CircleCI](https://circleci.com/gh/singularityware/docker2singularity.svg?style=svg)](https://circleci.com/gh/singularityware/docker2singularity)
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Are you developing Docker images and you would like to run them on an HPC cluster
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supporting [Singularity](https://www.sylabs.io/guides/2.5.1/user-guide/introduction.html)?
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Are you working on Mac or Windows with no easy access to a Linux machine? If the pull,
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build, and general commands to [work with docker images provided by Singularity](https://www.sylabs.io/guides/2.5.1/user-guide/singularity_and_docker.html?highlight=docker) natively do not fit your needs,
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`docker2singularity` is an alternative way to generate Singularity images.
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This particular branch is intended for Singularity 2.5.1, which gives you a selection of image formats to build.
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The containers are also available for you on [Docker Hub](https://hub.docker.com/r/singularityware/docker2singularity/).
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## Usage
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```
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docker run docker2singularity
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```bash
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docker run singularityware/docker2singularity
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USAGE: docker2singularity [-m "/mount_point1 /mount_point2"] [options] docker_image_name
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OPTIONS:
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## Inspect Your Image
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New with `docker2singularity` 2.4, the labels for the container are available with `inspect`:
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```
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```bash
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singularity inspect ubuntu_14.04-2017-09-13-3e51deeadc7b.simg
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{
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"org.label-schema.singularity.build": "squashfs",
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as is the runscript and environment
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```
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```bash
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singularity inspect --json -e -r ubuntu_14.04-2017-09-13-3e51deeadc7b.simg
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{
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"data": {
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## Build a Sandbox Image
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A sandbox image is a folder that is ideal for development. You can view it on your desktop, cd inside and browse, and it works like a Singularity image. To create a sandbox, specify the `-f` flag:
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```
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```bash
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docker run -v /var/run/docker.sock:/var/run/docker.sock \
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-v /host/path/change/me:/output \
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--privileged -t --rm \
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```
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Importantly, you can use `--writable`, and if needed, you can convert a sandbox folder into a production image:
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```
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```bash
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sudo singularity build sandbox/ production.simg
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```
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## Build a Legacy (ext3) Image
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You can build a legacy ext3 image (with `--writable`) with the `-w` flag. This is an older image format that is more prone to degradation over time, and (building) may not be supported for future versions of the software.
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```
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```bash
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docker run -v /var/run/docker.sock:/var/run/docker.sock \
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-v /host/path/change/me:/output \
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--privileged -t --rm \
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```
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You can also use `--writable` and convert an ext3 image into a production image:
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```
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```bash
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sudo singularity build ext3.img production.simg
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```
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### Contributed Examples
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The following are a list of brief examples and tutorials generated by the Singularity community for using **docker2singularity**. If you have an example of your own, please [let us know](https://www.github.com/singularityware/docker2singularity/issues)!
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- Don’t use the USER instruction set
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## FAQ
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Here are some frequently asked questions if you run into trouble!
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### "client is newer than server" error
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If you are getting the following error:
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`docker: Error response from daemon: client is newer than server`
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You need to use the `docker info` command to check your docker version and use it to grab the correct corresponding version of `docker2singularity`. For example:
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```bash
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docker run \
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-v /var/run/docker.sock:/var/run/docker.sock \
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-v D:\host\path\where\to\output\singularity\image:/output \
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--privileged -t --rm \
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singularityware/docker2singularity:1.11 \
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ubuntu:14.04
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```
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Currently only the 1.10, 1.11, 1.12, and 1.13 versions are supported. If you are using an older version of Docker you will need to upgrade.
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### My cluster/HPC requires Singularity images to include specific mount points
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If you are getting `WARNING: Non existant bind point (directory) in container: '/shared_fs'` or a similar error when running your Singularity image that means that your Singularity images require custom mount points. To make the error go away you can specify the mount points required by your system when creating the Singularity image:
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```bash
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docker run \
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-v /var/run/docker.sock:/var/run/docker.sock \
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-v D:\host\path\where\to\output\singularity\image:/output \
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--privileged -t --rm \
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singularityware/docker2singularity \
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-m "/shared_fs /custom_mountpoint2" \
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ubuntu:14.04
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```
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## Acknowledgements
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This work is heavily based on the `docker2singularity` work done by [vsoch](https://github.com/vsoch) and [gmkurtzer](https://github.com/gmkurtzer). Hopefully most of the conversion code will be merged into Singularity in the future making this container even leaner!
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This work is heavily based on the `docker2singularity` work done by [vsoch](https://github.com/vsoch)
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and [gmkurtzer](https://github.com/gmkurtzer). The original record of the work can be read about
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in [this commit](https://github.com/singularityware/docker2singularity/commit/d174cadefd90f77f302f4bef5a8cd089eb2da2e4).
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Thank you kindly to all the contributors, and please open an issue if you need help.

‎VERSION‎

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2.6

‎docker2singularity.sh‎

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# --- Option processing --------------------------------------------
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if [ $# == 0 ] ; then
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usage
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exit 1;
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exit 0;
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fi
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mount_points="/oasis /projects /scratch /local-scratch /work /home1 /corral-repl /corral-tacc /beegfs /share/PI /extra /data /oak"

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