Stop using Docker in Docker for container image (#690)

* maintenance: ignore some folders whith docker

* feature: simplify Dockerfiles

* fix: copy python libs correctly to image

* maintenance: make container to work in scripts

Because the tool containers are created by the host now, the folder
where the results are stored in the host needs to be mounted to the
cwltool container now.

* maintenance: update dockerfile metadata

MAINTAINER is deprecated, use LABEL instead

* fix: add wrapper to launch docker in a container

Adds 2 checks to see if it was correctly launched

* fix: enable build for cwltool_module image

* maintenance: remove trailing whitespace from windows doc

* maintenance: remove extraneous line from cwl-docker.sh

Author: undu

.dockerignore

@@ -0,0 +1,6 @@
+.tox/
+.eggs/
+.vscode/
+build/
+dist/
+*.Dockerfile

build-cwl-docker.sh

@@ -1,4 +1,4 @@
 #!/bin/sh
 set -e
-docker build --file=cwltool_module.Dockerfile --tag=commonworkflowlanguage/cwltool_module .
+docker build --file=cwltool.Dockerfile --tag=commonworkflowlanguage/cwltool-module --target module .
 docker build --file=cwltool.Dockerfile --tag=commonworkflowlanguage/cwltool .

cwl-docker.sh

@@ -1,3 +1,2 @@
 #!/bin/sh
-docker run --name=cwl-docker -v /var/lib/docker -i -t fedora-data true
-docker run --privileged -ti --volume=$PWD:$PWD -w=$PWD commonworkflowlanguage/cwltool $@
+exec docker run -v /var/run/docker.sock:/var/run/docker.sock -v /tmp:/tmp -v "$PWD":"$PWD" -w="$PWD" commonworkflowlanguage/cwltool "$@"

cwltool-in-docker.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env sh
+if [ ! -S /var/run/docker.sock ]; then
+  >&2 echo 'ERROR: cwltool cannot work inside a container without access to docker'
+  >&2 echo 'Launch the container with the option -v /var/run/docker.sock:/var/run/docker.sock'
+  exit 1
+elif [ "$PWD" = '/error' ]; then
+  >&2 echo 'ERROR: cwltool cannot work without access to the current path'
+  >&2 echo 'Launch the container with the options -v "$PWD":"$PWD" -w="$PWD"'
+  exit 1
+else
+  cwltool "$@"
+fi

cwltool.Dockerfile

@@ -1,21 +1,27 @@
-FROM commonworkflowlanguage/cwltool_module
-MAINTAINER [email protected]
-
-# Let's start with some basic stuff.
-RUN apt-get update -qq && apt-get install -qqy \
-    apt-transport-https \
-    ca-certificates \
-    curl \
-    lxc \
-    iptables \
-    python-setuptools
-
-# Install Docker from Docker Inc. repositories.
-RUN curl -sSL https://get.docker.com/ | sh
-
-# Install the magic wrapper.
-ADD ./wrapdocker /usr/local/bin/wrapdocker
-RUN chmod +x /usr/local/bin/wrapdocker
-
-VOLUME /var/lib/docker
-ENTRYPOINT ["wrapdocker", "cwltool"]
+FROM python:3.6-alpine as builder
+
+RUN apk add --no-cache git
+
+WORKDIR /cwltool
+COPY . .
+
+RUN python setup.py bdist_wheel --dist-dir=/wheels
+RUN pip wheel -r requirements.txt --wheel-dir=/wheels
+RUN pip install --no-index --no-warn-script-location --root=/pythonroot/ /wheels/*.whl
+
+FROM python:3.6-alpine as module
+LABEL maintainer [email protected]
+
+RUN apk add --no-cache docker nodejs
+COPY --from=builder /pythonroot/ /
+
+FROM python:3.6-alpine
+LABEL maintainer [email protected]
+
+RUN apk add --no-cache docker nodejs
+COPY --from=builder /pythonroot/ /
+COPY cwltool-in-docker.sh /cwltool-in-docker.sh
+
+WORKDIR /error
+
+ENTRYPOINT ["/cwltool-in-docker.sh"]

cwltool_module.Dockerfile

@@ -17,7 +17,7 @@ Quickstart Terminal.
 
 ## Installation
 
-You can install cwltool using pip or directly from source code.  
+You can install cwltool using pip or directly from source code.
 
 ### Requirements
 
@@ -37,13 +37,13 @@ pip install cwltool
 ### Install from source
 
 ```
-git clone https://github.com/common-workflow-language/cwltool.git  
-cd cwltool  
+git clone https://github.com/common-workflow-language/cwltool.git
+cd cwltool
 pip install .
 ```
 
 ***Note:*** In order to test if cwltool has been successfully installed on your
-Windows system, run `cwltool` in `cmd`. If you see help instructions, cwltool was successfully installed.  
+Windows system, run `cwltool` in `cmd`. If you see help instructions, cwltool was successfully installed.
 
 ```
    CWL document required, no input file was provided
@@ -78,12 +78,12 @@ python setup.py test
 To run the CWL conformance tests, follow these instructions:
 
 ```
-pip install cwltest mock 
-git clone https://github.com/common-workflow-language/common-workflow-language.git   
-cd common-workflow-language/v1.0  
+pip install cwltest mock
+git clone https://github.com/common-workflow-language/common-workflow-language.git
+cd common-workflow-language/v1.0
 cwltest --test conformance_test_v1.0.yaml -j 4 --tool cwltool
 ```
-The `-j` options is used to run multiple tests in parallel.  
+The `-j` options is used to run multiple tests in parallel.
 
 ## Troubleshooting
 
@@ -97,19 +97,19 @@ consulting the [online Docker Community](https://forums.docker.com/).
 
 ### Your local drives are not being shared with Docker Containers
 
-* ***On native Docker for Windows (supported by Windows 10):***  
-On your tray, next to your clock, right-click on Docker, then click on Settings,  
-there you'll find the shared rdives: Here you can share your drives with Docker.  
+* ***On native Docker for Windows (supported by Windows 10):***
+On your tray, next to your clock, right-click on Docker, then click on Settings,
+there you'll find the shared rdives: Here you can share your drives with Docker.
 If you encounter a problem with your firewall, please
 [refer this to post](https://blog.olandese.nl/2017/05/03/solve-docker-for-windows-error-a-firewall-is-blocking-file-sharing-between-windows-and-the-containers/).
 
-* ***On Docker Toolbox:***  
-Docker Toolbox uses Virtualbox to create a linux base on which Docker machine runs.  
-Your Docker Container will be created inside Virtualbox. To share drives  
+* ***On Docker Toolbox:***
+Docker Toolbox uses Virtualbox to create a linux base on which Docker machine runs.
+Your Docker Container will be created inside Virtualbox. To share drives
 in virtualbox, go to ****Virtualbox->settings->shared folders->Machine Folders****
-Here Map the drives you want to share with your Docker Container.  
-If you want to keep these settings permanent (Recommended!), You should mark the  
-`make permanent` checkbox or else these settings will be erased every time your  
+Here Map the drives you want to share with your Docker Container.
+If you want to keep these settings permanent (Recommended!), You should mark the
+`make permanent` checkbox or else these settings will be erased every time your
 virtualbox closes.
 
 ### In a Docker Container with shared drives, not all files are shown on `ls`
@@ -127,7 +127,7 @@ on your local machine, you should be able to write to that folder inside Docker
 Container also (provided same user initiated Docker). In all it is a file
 permission issue.
 
-### Workflows with Javascript Expressions occasionally give Timeout errors  
+### Workflows with Javascript Expressions occasionally give Timeout errors
 To evaluate Javascript Expressions, cwltool looks for Nodejs on your system.
 In case Nodejs isn't installed, JS expressions are executed in a Docker Container.
 In order to avoid waiting forever in case error occurs, cwltool times out js