---
layout: default
navsection: userguide
-title: "Customizing Crunch environment using Docker"
+title: "Working with Docker images"
...
+{% comment %}
+Copyright (C) The Arvados Authors. All rights reserved.
-This page describes how to customize the runtime environment (e.g. the programs, libraries, and other dependencies needed to run a job) that a crunch script will be run in using "Docker.":https://www.docker.com/ Docker is a tool for building and running containers that isolate applications from other applications running on the same node. For detailed information about Docker, see the "Docker User Guide.":https://docs.docker.com/userguide/
+SPDX-License-Identifier: CC-BY-SA-3.0
+{% endcomment %}
-This page will demonstrate how to:
+This page describes how to set up the runtime environment (e.g., the programs, libraries, and other dependencies needed to run a job) that a workflow step will be run in using "Docker.":https://www.docker.com/ Docker is a tool for building and running containers that isolate applications from other applications running on the same node. For detailed information about Docker, see the "Docker User Guide.":https://docs.docker.com/userguide/
-# Fetch the arvados/jobs Docker image
-# Manually install additional software into the container
-# Create a new custom image
-# Upload that image to Arvados for use by Crunch jobs
-# Share your image with others
+This page describes:
+
+# "Create a custom image using a Dockerfile":#create
+# "Uploading an image to Arvados":#upload
+# "Sources of pre-built bioinformatics Docker images":#sources
{% include 'tutorial_expectations_workstation' %}
You also need ensure that "Docker is installed,":https://docs.docker.com/installation/ the Docker daemon is running, and you have permission to access Docker. You can test this by running @docker version@. If you receive a permission denied error, your user account may need to be added to the @docker@ group. If you have root access, you can add yourself to the @docker@ group using @$ sudo addgroup $USER docker@ then log out and log back in again; otherwise consult your local sysadmin.
-h2. Fetch a starting image
+h2(#create). Create a custom image using a Dockerfile
-The easiest way to begin is to start from the "arvados/jobs" image which already has the Arvados SDK installed along with other configuration required for use with Crunch.
+This example shows how to create a Docker image and add the R package.
-Download the latest "arvados/jobs" image from the Docker registry:
+First, create new directory called @docker-example@, in that directory create a file called @Dockerfile@.
<notextile>
-<pre><code>$ <span class="userinput">docker pull arvados/jobs:latest</span>
-Pulling repository arvados/jobs
-3132168f2acb: Download complete
-a42b7f2c59b6: Download complete
-e5afdf26a7ae: Download complete
-5cae48636278: Download complete
-7a4f91b70558: Download complete
-a04a275c1fd6: Download complete
-c433ff206a22: Download complete
-b2e539b45f96: Download complete
-073b2581c6be: Download complete
-593915af19dc: Download complete
-32260b35005e: Download complete
-6e5b860c1cde: Download complete
-95f0bfb43d4d: Download complete
-c7fd77eedb96: Download complete
-0d7685aafd00: Download complete
+<pre><code>$ <span class="userinput">mkdir docker-example-r-base</span>
+$ <span class="userinput">cd docker-example-r-base</span>
</code></pre>
</notextile>
-h2. Install new packages
-
-Next, enter the container using @docker run@, providing the arvados/jobs image and the program you want to run (in this case the bash shell).
-
<notextile>
-<pre><code>$ <span class="userinput">docker run --interactive --tty --user root arvados/jobs /bin/bash</span>
-root@a0e8299b59aa:/#
+<pre><code>FROM ubuntu:bionic
+RUN apt-get update && apt-get -yq --no-install-recommends install r-base-core
</code></pre>
</notextile>
-Next, update the package list using @apt-get update@.
+The "RUN" command is executed inside the container and can be any shell command line. You are not limited to installing Debian packages. You may compile programs or libraries from source and install them, edit systemwide configuration files, use other package managers such as @pip@ or @gem@, and perform any other customization necessary to run your program.
-<notextile>
-<pre><code>root@a0e8299b59aa:/# <span class="userinput">apt-get update</span>
-Get:1 http://apt.arvados.org wheezy Release.gpg [490 B]
-Get:2 http://apt.arvados.org wheezy Release [1568 B]
-Get:3 http://apt.arvados.org wheezy/main amd64 Packages [34.6 kB]
-Get:4 http://ftp.us.debian.org wheezy Release.gpg [1655 B]
-Get:5 http://ftp.us.debian.org wheezy-updates Release.gpg [836 B]
-Get:6 http://ftp.us.debian.org wheezy Release [168 kB]
-Ign http://apt.arvados.org wheezy/main Translation-en
-Get:7 http://security.debian.org wheezy/updates Release.gpg [836 B]
-Get:8 http://security.debian.org wheezy/updates Release [102 kB]
-Get:9 http://ftp.us.debian.org wheezy-updates Release [124 kB]
-Get:10 http://ftp.us.debian.org wheezy/main amd64 Packages [5841 kB]
-Get:11 http://security.debian.org wheezy/updates/main amd64 Packages [218 kB]
-Get:12 http://security.debian.org wheezy/updates/main Translation-en [123 kB]
-Hit http://ftp.us.debian.org wheezy/main Translation-en
-Hit http://ftp.us.debian.org wheezy-updates/main amd64 Packages/DiffIndex
-Hit http://ftp.us.debian.org wheezy-updates/main Translation-en/DiffIndex
-Fetched 6617 kB in 5s (1209 kB/s)
-Reading package lists... Done
-</code></pre>
-</notextile>
+You can also visit the "Docker tutorial":https://docs.docker.com/get-started/part2/ for more information and examples.
+
+You should add your Dockerfiles to the same source control repository as the Workflows that use them.
-In this example, we will install the "R" statistical language Debian package "r-base-core". Use @apt-get install@:
+h3. Create a new image
+
+We're now ready to create a new Docker image. Use @docker build@ to create a new image from the Dockerfile.
<notextile>
-<pre><code>root@a0e8299b59aa:/# <span class="userinput">apt-get install r-base-core</span>
-Reading package lists... Done
-Building dependency tree
-Reading state information... Done
-The following extra packages will be installed:
- [...]
-libxv1 libxxf86dga1 libxxf86vm1 r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster r-cran-codetools
- [...]
-Suggested packages:
- [...]
-The following NEW packages will be installed:
- [...]
- libxv1 libxxf86dga1 libxxf86vm1 r-base r-base-core r-base-dev r-base-html r-cran-boot r-cran-class r-cran-cluster
- [...]
-0 upgraded, 107 newly installed, 0 to remove and 9 not upgraded.
-Need to get 88.2 MB of archives.
-After this operation, 219 MB of additional disk space will be used.
-Do you want to continue [Y/n]? y
-[...]
-Get:85 http://ftp.us.debian.org/debian/ wheezy/main r-base-core amd64 2.15.1-4 [20.6 MB]
-Get:86 http://ftp.us.debian.org/debian/ wheezy/main r-base-dev all 2.15.1-4 [3882 B]
-Get:87 http://ftp.us.debian.org/debian/ wheezy/main r-cran-boot all 1.3-5-1 [472 kB]
-[...]
-Fetched 88.2 MB in 2min 17s (642 kB/s)
-Extracting templates from packages: 100%
-Preconfiguring packages ...
-[...]
-Unpacking r-base-core (from .../r-base-core_2.15.1-4_amd64.deb) ...
-Selecting previously unselected package r-base-dev.
-Unpacking r-base-dev (from .../r-base-dev_2.15.1-4_all.deb) ...
-Selecting previously unselected package r-cran-boot.
-Unpacking r-cran-boot (from .../r-cran-boot_1.3-5-1_all.deb) ...
-[...]
-Setting up r-base-core (2.15.1-4) ...
-Setting R_PAPERSIZE_USER default to 'a4'
-
-Creating config file /etc/R/Renviron with new version
-Setting up r-base-dev (2.15.1-4) ...
-Setting up r-cran-boot (1.3-5-1) ...
-[...]
+<pre><code>docker-example-r-base$ <span class="userinput">docker build -t docker-example-r-base .</span>
</code></pre>
</notextile>
+h3. Verify image
+
Now we can verify that "R" is installed:
<notextile>
-<pre><code>root@a0e8299b59aa:/# <span class="userinput">R</span>
+<pre><code>$ <span class="userinput">docker run -ti docker-example-r-base</span>
+root@57ec8f8b2663:/# R
-R version 2.15.1 (2012-06-22) -- "Roasted Marshmallows"
-Copyright (C) 2012 The R Foundation for Statistical Computing
-ISBN 3-900051-07-0
+R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
+Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
-
-R is free software and comes with ABSOLUTELY NO WARRANTY.
-You are welcome to redistribute it under certain conditions.
-Type 'license()' or 'licence()' for distribution details.
-
-R is a collaborative project with many contributors.
-Type 'contributors()' for more information and
-'citation()' on how to cite R or R packages in publications.
-
-Type 'demo()' for some demos, 'help()' for on-line help, or
-'help.start()' for an HTML browser interface to help.
-Type 'q()' to quit R.
-
->
</code></pre>
</notextile>
-Note that you are not limited to installing Debian packages. You may compile programs or libraries from source and install them, edit systemwide configuration files, use other package managers such as @pip@ or @gem@, and perform any other customization necessary to run your program.
+h2(#upload). Upload your image
-h2. Create a new image
-
-We're now ready to create a new Docker image. First, quit the container, then use @docker commit@ to create a new image from the stopped container. The container id can be found in the default hostname of the container displayed in the prompt, in this case @a0e8299b59aa@:
+Finally, we are ready to upload the new Docker image to Arvados. Use @arv-keepdocker@ with the image repository name to upload the image. Without arguments, @arv-keepdocker@ will print out the list of Docker images in Arvados that are available to you.
<notextile>
-<pre><code>root@a0e8299b59aa:/# <span class="userinput">exit</span>
-$ <span class="userinput">docker commit a0e8299b59aa arvados/jobs-with-r</span>
-33ea6b87792364cb9989a149c36a31e5a9c8cf96694ba05f66545ad7b842522e
-$ <span class="userinput">docker images</span>
-REPOSITORY TAG IMAGE ID CREATED VIRTUAL SIZE
-arvados/jobs-with-r latest 33ea6b877923 43 seconds ago 1.607 GB
-arvados/jobs latest 3132168f2acb 22 hours ago 1.314 GB
-</code></pre>
-</notextile>
-
-h2. Upload your image
+<pre><code>$ <span class="userinput">arv-keepdocker docker-example-r-base</span>
+2020-06-29 13:48:19 arvados.arv_put[769] INFO: Creating new cache file at /home/peter/.cache/arvados/arv-put/39ddb51ebf6c5fcb3d713b5969466967
+206M / 206M 100.0% 2020-06-29 13:48:21 arvados.arv_put[769] INFO:
-Finally, we are ready to upload the new Docker image to Arvados. Use @arv keep docker@ with the image repository name to upload the image. Without arguments, @arv keep docker@ will print out the list of Docker images in Arvados that are available to you.
+2020-06-29 13:48:21 arvados.arv_put[769] INFO: Collection saved as 'Docker image docker-example-r-base:latest sha256:edd10'
+x20vs-4zz18-0tayximqcyb6uf8
-<notextile>
-<pre><code>$ <span class="userinput">arv keep docker arvados/jobs-with-r</span>
-1591M / 1591M 100.0%
-Collection saved as 'Docker image arvados/jobs-with-r:latest 33ea6b877923'
-qr1hi-4zz18-3fk2px2ji25nst2
-$ <span class="userinput">arv keep docker</span>
+$ <span class="userinput">arv-keepdocker images</span>
REPOSITORY TAG IMAGE ID COLLECTION CREATED
-arvados/jobs-with-r latest 33ea6b877923 qr1hi-4zz18-3fk2px2ji25nst2 Thu Oct 16 13:58:53 2014
+docker-example-r-base latest sha256:edd10 x20vs-4zz18-0tayximqcyb6uf8 Mon Jun 29 17:46:16 2020
</code></pre>
</notextile>
-You are now able to specify the runtime environment for your program using the @docker_image@ field of the @runtime_constaints@ section of your pipeline components:
+You are now able to specify the runtime environment for your program using @DockerRequirement@ in your workflow:
-<notextile>
-{% code 'example_docker' as javascript %}
-</notextile>
+<pre>
+hints:
+ DockerRequirement:
+ dockerPull: docker-example-r-base
+</pre>
-* The @docker_image@ field can be one of: the Docker repository name (as shown above), the Docker image hash, or the Arvados collection portable data hash.
+h3. Uploading Docker images to a shared project
-h2. Share Docker images
-
-Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others (or wish to share a pipeline template that uses your Docker image) you will need to use @arv keep docker@ with the @--project-uuid@ option to upload the image to a shared project.
+Docker images are subject to normal Arvados permissions. If wish to share your Docker image with others you should use @arv-keepdocker@ with the @--project-uuid@ option to add the image to a shared project and ensure that metadata is set correctly.
<notextile>
-<pre><code>$ <span class="userinput">arv keep docker --project-uuid qr1hi-j7d0g-xxxxxxxxxxxxxxx arvados/jobs-with-r</span>
+<pre><code>$ <span class="userinput">arv-keepdocker docker-example-r-base --project-uuid zzzzz-j7d0g-xxxxxxxxxxxxxxx</span>
</code></pre>
</notextile>
+
+h2(#sources). Sources of pre-built images
+
+In addition to creating your own contianers, there are a number of resources where you can find bioinformatics tools already wrapped in container images:
+
+"BioContainers":https://biocontainers.pro/
+
+"Dockstore":https://dockstore.org/
+
+"Docker Hub":https://hub.docker.com/
projects / arvados.git / blobdiff