Creating a Dockerfile

Intro:

Now that you have your container working, you need to make a Dockerfile. iPlant won’t pull your image from hub.docker because they have no idea what you’ve put in it. Instead, iPlant wants a Dockerfile that is used to build your container. This is basically the steps you used get your previous container working, but in a single file. They aren’t too hard to make, just follow some best practices and iPlant will be happy.

Details on building images with a Dockerfile: https://docs.docker.com/reference/builder/
Best practices for making a Dockerfile: https://docs.docker.com/articles/dockerfile_best-practices/

Steps:

Write your Dockerfile

Dockerfile for hisat2 based on ubuntu 14.04.3

Dockerfile

        FROM ubuntu:14.04.3
        MAINTAINER Eric Lyons
        RUN apt-get update && apt-get install -y \
          build-essential \
          git \
          python

        ENV BINPATH /usr/bin
        ENV SRCPATH /usr/src
        ENV HISAT2GIT https://github.com/infphilo/hisat2.git
        ENV HISAT2PATH $SRCPATH/hisat2
        
        RUN mkdir -p $SRCPATH 
        WORKDIR $SRCPATH
        RUN git clone "$HISAT2GIT"
        RUN make -C $HISAT2PATH \
          && cp $HISAT2PATH/hisat2 $BINPATH \
          && cp $HISAT2PATH/hisat2-* $BINPATH
        
        ENTRYPOINT ["/usr/bin/hisat2"]

Note: There are options to define default behavior of Docker Image when run.
1. ENTRYPOINT defines what should be run when the image is run, and is ideal when a tool consists of a single main program.
2. CMD can also be added to define default arguments to pass to the entrypoint when none are provided; frequently this is used to pass e.g. "–help" by default

To build your docker image:
1. ```
docker build <directory with Dockerfile>
```
2. Note: You can add the option: -t <tag> to create an easier to use name for using the docker image
Once built, you can test
1. ```
docker run <image number>
```

Next Step