---
layout: default
navsection: userguide
title: "Customizing the Crunch runtime environment"
...
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/
This page will demonstrate:
# How to 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.
{% include 'tutorial_expectations' %}
h2. Fetching a starting image
First, download the latest image from the Docker registry:
$ docker pull arvados/jobs
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
h2. Installing new packages
Next, enter the container using "docker run", the arvados/jobs image, and the program you want to run (in this case the bash shell).
$ docker run --interactive --tty --user root arvados/jobs /bin/bash
root@a0e8299b59aa:/#
Next, update the package list using @apt-get update@.
root@a0e8299b59aa:/# apt-get update
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
In this example, we will install the "R" statistical language Debian package "r-base-core". Use @apt-get install@:
root@a0e8299b59aa:/# apt-get install r-base-core
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) ...
[...]
Now we can verify that "R" is installed:
root@a0e8299b59aa:/# 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
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.
>
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@:
root@a0e8299b59aa:/# exit
$ docker commit a0e8299b59aa arvados/jobs-with-r
33ea6b87792364cb9989a149c36a31e5a9c8cf96694ba05f66545ad7b842522e
$ docker images
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
h2. Upload your image
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.
$ arv keep docker arvados/jobs-with-r
1591M / 1591M 100.0%
Collection saved as 'Docker image arvados/jobs-with-r:latest 33ea6b877923'
qr1hi-4zz18-3fk2px2ji25nst2
$ arv keep docker
REPOSITORY TAG IMAGE ID COLLECTION CREATED
arvados/jobs-with-r latest 33ea6b877923 qr1hi-4zz18-3fk2px2ji25nst2 Thu Oct 16 13:58:53 2014
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:
{% code 'example_docker' as javascript %}