Docker builds for rDock docking program

For details about rDock look here

Code changes

Note: the rDock source code is modified slightly to remove the check that the ligand structures are 3D structures. The way that rDock does this check is very picky and often real 3D structures fail this check. A better solution is needed for this. See this commit for the changes.

Kitchen sink image

This was the original rDock image that we created. We call it a kitchen sink image as the image contains not only the rDock binaries but also the entire build infrastructure that was needed to compile it. This includes gcc, make and a raft of other things. It also includes runtime tools such as Python and OpenBabel. The consequence of this is that whilst you end up with an image that contains lots of useful goodies and might be useful for hacking, it comes in at ~500MB in size, which not only means it takes a long time to pull over the internet, but it has a large attack surface for hackers to try to get into, and so it makes a poor image for running production systems that will be public facing. See below for the more recent buildah-based images that are much better suited to production use.

• Dockerfile is a build for rdock. Find image on Dockerhub at informaticsmatters/rdock.
• nextflow/Dockerfile also contains Nextflow which is useful for running more complex pipelines. Find image on Dockerhub at informaticsmatters/rdock_nextflow.

Buildah images

In contrast to the kitchen sink images we also create minimal images using the buildah tool. These images are named informaticsmatters/rdock-mini. The general concept has been described in the smaller containers series of posts on the Informatics Matters blog.

These images contain only a minimal centos:7 operating system, a few standard Linux utilities (bash, procps-ng and the coreutils packages), the popt runtime library needed by rDock, and Perl (as rDock includes some Perl scripts). The result is an image that is only ~100MB in size, ~5x smaller than the kitchen sink image.

To build this image:

Step 1

Build the Docker image from which we are going to build the buildah-mini image. This is based on a Centos7 image and contains all the build infrastructure that is needed to build rDock from the source code.

docker build -f Dockerfile-buildah -t informaticsmatters/rdock-buildah .

Step 2

Use this image to build the buildah binaries and load these into a minimal Centos7 based image:

sudo ./build.sh

This does 2 things:

1. Fires up the container and executes the buildah-build.sh script that compiles the code and uses buildah to create a new image containing the rdlock binaries.
2. Push that buildah image to a local Docker image named informaticsmatters/rdock-mini so that it can also be run from docker.

### Step 3 
Optionally push the image to Docker Hub:

docker push informaticsmatters/rdock-mini:latest

You need the necessary privileges for this. The image can be found on Docker Hub at 
[informaticsmatters/rdock-mini/](https://hub.docker.com/r/informaticsmatters/rdock-mini/).

### Running the image

To run the image you might want to allow to access your current directory and run as your user ID.
Try something like this:

$ docker run -it --rm -u $(id -u):$(id -g) -v $PWD:$PWD:Z -w $PWD informaticsmatters/rdock-mini bash bash-4.2# rbdock

---

The rDock program is licensed under GNU-LGPLv3.0. http://rdock.sourceforge.net/ Executable: rbdock ($Id: //depot/dev/client3/rdock/2013.1/src/exe/rbdock.cxx#4 $) Library: libRbt.so/2013.1/901 2013/11/27 RBT_ROOT: /rDock_2013.1 RBT_HOME: /root Current dir: / Date: Sun Jun 17 13:08:51 2018

---

Usage: rbdock -i -o -r -p [-n ] [-ap] [-an] [-allH] [-t <targetScore|targetFilterFile>] [-c] [-T ] [-s ]

Options: -i - input ligand SD file -o - root name for output file(s) -r - receptor parameter file -p - docking protocol parameter file -n - number of runs/ligand (default=1) -ap - protonate all neutral amines, guanidines, imidazoles (default=disabled) -an - deprotonate all carboxylic, sulphur and phosphorous acid groups (default=disabled) -allH - read all hydrogens present (default=polar hydrogens only) -t - score threshold OR filter file name -c - continue if score threshold is met (use with -t , default=terminate ligand) -T - controls output level for debugging (0 = minimal, >0 = more verbose) -s - random number seed (default=from sys clock) bash-4.2#

By default the container runs as the root user but you can (and should) run the container as a non-priviledged user.
Any user ID can be used, including a randomly assigned ID.