docknitr: Making a Custom Image

Ben Artin

2020-01-08

Making custom images

One of Docker’s superpowers is the ability to easily make custom images. The full range of capabilities of custom Docker images is far beyond the scope of this documentation, but the short version is that to make a custom image you need to take two steps: first, you create a file ( called Dockerfile) that contains instructions for how to build a custom image based on an existing image.

For example, the base Python image does not contain the munch Python package:

```{r engine="docker", image="python:3", error=TRUE}
import munch
print(munch.__version__)
```
#> Traceback (most recent call last):
#>   File "<stdin>", line 1, in <module>
#> ModuleNotFoundError: No module named 'munch'

To create a custom image in which you have Python 3 with the munch Python package preinstalled, you might create a Dockerfile as follows:

FROM python:3
RUN pip install munch

This file should be named Dockerfile and live in a folder by itself; let’s call that folder python3-munch. You can think of a Dockerfile as computer-readable installation instructions.

The second step is to turn these installation instructions into a Docker image, and tag this custom image. This is accomplished using a Terminal command like this one:

docker build --tag python3-munch python3-munch
#> Sending build context to Docker daemon  2.048kB


#> Step 1/2 : FROM python:3
#>  ---> 1f88553e8143
#> Step 2/2 : RUN pip install munch
#>  ---> Running in 9c547480cfb4
#> Collecting munch
#>   Downloading https://files.pythonhosted.org/packages/cc/ab/85d8da5c9a45e072301beb37ad7f833cd344e04c817d97e0cc75681d248f/munch-2.5.0-py2.py3-none-any.whl
#> Collecting six
#>   Downloading https://files.pythonhosted.org/packages/65/26/32b8464df2a97e6dd1b656ed26b2c194606c16fe163c695a992b36c11cdf/six-1.13.0-py2.py3-none-any.whl
#> Installing collected packages: six, munch
#> Successfully installed munch-2.5.0 six-1.13.0
#> Removing intermediate container 9c547480cfb4
#>  ---> f83c7523a7e2
#> Successfully built f83c7523a7e2
#> Successfully tagged python3-munch:latest

The first parameter is the tag you want to give your custom image, and the second is the name of the folder containing the Dockerfile. In our case, both are python3-munch.

If you look through the output of that command, you will see that Docker creates a new image by starting from the existing python:3 image, and then running the commands you gave it in the Dockerfile; the result of that process is saved under the tag you specified.

Having done so, you can use your tagged custom image from Rmarkdown:

```{r engine="docker", image="python3-munch"}
import munch
print(munch.__version__)
```
#> 2.5.0

pyseer

To give a less contrived example, let’s make a custom image for pyseer, a genome-wide association studies Python package. If you look through pyseer documentation and tutorials, you will see that it relies heavily on Unix terminal commands (aka shell commands), so a good way to make this image would be to start with a Unix system, install pyseer in it, and then use a Unix shell (such as bash) to run pyseer.

How to work out the details of installing pyseer is beyond the scope of this vignette, but since I already worked out those details, I can share them with you in the form of a Dockerfile — and you can use this Dockerfile without deep knowledge of how I came up with it (it involved pyseer documentation, and frustration). Make a new folder named pyseer, and create a file named Dockerfile inside it with the following contents:

FROM ubuntu:19.04
RUN apt-get -qq update && apt-get -qq install --yes --no-install-recommends \
  wget \
  python3-setuptools \
  python3-wheel \
  python3-pip \
  python3-numpy \
  python3-scipy \
  python3-statsmodels \
  python3-pysam \
  python3-pybedtools \
  mash \
  > /dev/null
RUN pip3 install --quiet glmnet_py pyseer

This Dockerfile starts from Ubuntu Linux (version 19.04), installs all the prerequisites of pyseer according to the pyseer installation instructions, and then installs pyseer itself.

It also installs the mash utility (which the pyseer tutorial uses) and the wget utility (which is used to download the pyseer tutorial data files); these utilities could have been installed in their separate Docker images, but for the purpose of this exercise, that would have just added unnecessary complexity.s

The main strength of using Docker for this kind of work is that a Dockerfile contains computer-readable installation instructions, and therefore it takes away all the problems of “did you follow the installation instructions correctly”. Only one person needs to write a Dockerfile, which they can then share with others to let them install whatever software packages they all need to use.

Build your new image and tag it with pyseer. This will take a few minutes — there’s lots of downloading and installing to be done:

docker build --tag pyseer pyseer
#> Sending build context to Docker daemon  2.048kB


#> Step 1/3 : FROM ubuntu:19.04
#>  ---> 703d46da649e
#> Step 2/3 : RUN apt-get -qq update && apt-get -qq install --yes --no-install-recommends   wget   python3-setuptools   python3-wheel   python3-pip   python3-numpy   python3-scipy   python3-statsmodels   python3-pysam   python3-pybedtools   mash   > /dev/null
#>  ---> Running in 0360d27fe1d9
#> debconf: delaying package configuration, since apt-utils is not installed
#> Removing intermediate container 0360d27fe1d9
#>  ---> 9372dbd25ee9
#> Step 3/3 : RUN pip3 install --quiet glmnet_py pyseer
#>  ---> Running in ebe29ca62954
#> Removing intermediate container ebe29ca62954
#>  ---> 4b5d1db97dd3
#> Successfully built 4b5d1db97dd3
#> Successfully tagged pyseer:latest

Congratulations, you have pyseer! You can run it from RStudio:

```{r engine="docker", image="pyseer", command="bash", share.files=TRUE}
pyseer --version
```
#> pyseer 1.3.4

While we are here, let’s make an alias for it:

docknitr::docker_alias("pyseer", image="pyseer", command="bash", share.files=TRUE)

Your next step is probably to run the pyseer tutorial. You can now run the following code (using the pyseer Docker image) to download pyseer_tutorial.tar.bz2 and extract the data files (which takes a while):

```{pyseer}
mkdir pyseer-tutorial
cd pyseer-tutorial
wget --continue --no-verbose --output-document=pyseer_tutorial.tar.bz2 https://ndownloader.figshare.com/files/14091179
tar xvf pyseer_tutorial.tar.bz2
mkdir assemblies
cd assemblies
tar xf ../assemblies.tar.bz2
```
#> assemblies.tar.bz2
#> fsm_file_list.txt
#> snps.vcf.gz
#> gene_presence_absence.Rtab
#> core_genome_aln.tree
#> resistances.pheno
#> mash_sketch.msh
#> Spn23F.fa
#> Spn23F.gff
#> 6952_7#3.fa
#> 6952_7#3.gff

Now you’re finally ready to run the first step of data analysis, again using the pyseer image in Docker:

```{pyseer}
cd pyseer-tutorial
mash sketch -s 10000 -o mash_sketch assemblies/*.fa
mash dist mash_sketch.msh mash_sketch.msh| square_mash > mash.tsv
scree_plot_pyseer mash.tsv
```
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#> Writing to mash_sketch.msh...
#> Plotting only the first 30 eigenvalues out of 276

And now you have a scree plot!

knitr::include_graphics("pyseer-tutorial/scree_plot.png")
Scree plot from pyseer

Scree plot from pyseer

The remainder of the pyseer tutorial is left as an exercise for the reader 🙂