LoamStream Docker Images

The Loam Docker images are broken up into three images (see below for details on each).

In order to build these images, you will need to have Docker installed (the CE edition is fine).

Building the Images

The base Docker image used for these images is ubuntu:xenial (16.04). The images are built - in order - one at a time, as each depends on the previous one. Once one is built once, there's no need to build it again unless the Dockerfile for it has been updated.

```bash

First build the python27 image

docker build --tag broadinstitute/dig-loam:python27 --force-rm python27

Next, build the r34 image

docker build --tag broadinstitute/dig-loam:r34 --force-rm r34

Finally, build the tools image

docker build --tag broadinstitute/dig-loam:tools --force-rm tools ```

To see the images, run docker images:

REPOSITORY TAG IMAGE ID ... broadinstitute/dig-loam universal 11873c3d0b78 broadinstitute/dig-loam r34 e8625624bd7d broadinstitute/dig-loam python27 138d26c94857 ubuntu xenial 0b1edfbffd27

To test one of the images, you need to create a container from it and start it.

```bash

create a new container from the python image

$ docker create broadinstitute/dig-loam:python27 python -c "print('Hello, world!')" 1c55cc80825eb73e82e6615a216ebda78907eba1559ba05f330bc1620061edc5

show the container list and that it was created

$ docker ps -a CONTAINER ID IMAGE COMMAND CREATED STATUS 1c55cc80825e broadinstitute/dig-loam:python27 "python -c 'print('H…" 3 seconds ago Created

start the container, attach STDOUT to see the output

$ docker start -a 1c55cc80825e Hello, world!

get rid of the stopped container now that we don't need it

$ docker rm 1c55cc80825e ```

Pushing an Image to DockerHub

Log into docker:

bash $ docker login

Push an image:

bash $ docker push broadinstitute/dig-loam:python27 $ docker push broadinstitute/dig-loam:r34 $ docker push broadinstitute/dig-loam:tools

Sharing an Image

If you don't wish to publish the images, but would like to share one, you can use Docker to create a TAR from an image and send it (e.g. via FTP) to another to use:

bash docker save -o loam_tools.tar loam:tools

Conversely, once received, the image can be loaded using Docker by the receipient:

bash docker load < loam_tools.tgz

For more details/examples, see: Docker save and Docker load.

Image: loam:python27

This image has Python 2.7 and all the dependencies required for the LoamStream pipeline to run. It is the root image that the other images require.

• numpy
• pandas
• scipy
• matplotlib
• seaborn
• pysam
• ghostscript
• decorator

Image: loam:r34

This image is built from loam:python27 and adds R 3.4 along with all the CRAN and Bioconductor packages required.

CRAN Packages

• argparse
• caret
• corrplot
• ggplot2
• gridExtra
• gtable
• reshape2
• UpSetR

Bioconductor Packages

• gdsfmt
• GENESIS
• GWASTools
• SNPRelate

Image: loam:tools

This is the full image, build from loam:r34 that has all the additional binaries and scripts installed that are used by the LoamStream pipeline.

Additional Tools/Scripts

• bcftools
• ghostscript
• htslib
• king
• klustakwik
• liftover
• locuszoom
• new_fugue
• pdflatex
• plink
• samtools

Note: LocusZoom is installed in program-form only! It does not contain the reference genome!

Image: loam:hail

This is the full image, build from loam:tools containing hail and its prerequisites.

Additional Tools/Scripts

• Java JDK
• Spark
• hail 0.1

_Note: Some environment variables are also updated as required by hail