I'm at the PyCon 2015 sprints (day 2), and I took the opportunity to play around with Docker a bit.

First, I created a local docker container that contained an installed version of khmer. I ran a blank docker container:

docker run -it ubuntu

and then installed the khmer prereqs on it, followed by khmer (run on the docker container):

apt-get update
apt-get install -y python-pip python-dev
pip install khmer

then I logged out, and created a named docker container from that:

docker commit -m "installed khmer" -a "Titus Brown" 28138ab4095d titus/khmer:v1.3

And now I can run the khmer scripts like this --

docker run -it titus/khmer:v1.3 /usr/local/bin/normalize-by-median.py

Next, I automated all of this with a Dockerfile:

cat > Dockerfile <<EOF
FROM ubuntu:14.04
MAINTAINER Titus Brown <titus@idyll.org>
RUN apt-get update && apt-get install -y python-dev python-pip
RUN pip install -U setuptools
RUN pip install khmer==1.3
EOF

docker build -t titus/khmer:v1.3 .

Either container lets me run normalize by median on a file outside of the container like so:

mkdir foo
curl https://raw.githubusercontent.com/ged-lab/khmer/master/data/100k-filtered.fa > foo/sequence.fa

docker run -v $PWD/foo:/data -it titus/khmer:v1.3 normalize-by-median.py /data/sequence.fa -o /data/result.fa

Here, I'm running 'normalize-by-median' on the input file 'foo/sequence.fa', and the output is placed in 'foo/result.fa'. The trick is that the './foo/' directory is mounted on the docker container as '/data/', so normalize-by-median.py sees it as '/data/sequence.fa'.

Nice and easy, so far...

--titus