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Creating a Dockerfile

Creating a Dockerfile

Oct 05, 2015

 

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.

 

  1. Details on building images with a Dockerfile: https://docs.docker.com/reference/builder/

  2. Best practices for making a Dockerfile: https://docs.docker.com/articles/dockerfile_best-practices/

Steps:

  1. Write your Dockerfile

  2. Dockerfile for hisat2 based on ubuntu 14.04.3

    1. Dockerfile

    2. 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"]

    3. 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

  3. 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

  4. Once built, you can test 

    1. docker run <image number>

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