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Add example: reproducing an analysis with one Docker command #218

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27 changes: 27 additions & 0 deletions _episodes/docker-image-examples.md
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Expand Up @@ -57,6 +57,33 @@ following resources show what it can look like:
- [Introduction to Singularity](https://carpentries-incubator.github.io/singularity-introduction/): See the episode titled "Running MPI parallel jobs using Singularity containers"
- [Container Workflows at Pawsey](https://pawseysc.github.io/container-workflows/): See the episode titled "Run containers on HPC with Shifter (and Singularity)"

## Reproducible analysis with one command

In this example of a published study using Docker, the user only has to run one
command to reproduce the entire analysis:

~~~
docker run --rm -v ${PWD}:/wd -w /wd joelnitta/pleurosoriopsis:targets \
bash /tmp/make.sh
~~~
{: .language-bash}

The Docker image contains a shell script, `make.sh`, which downloads the
analysis source code using `git clone`, then runs the analysis.

The source code will be downloaded to a folder called `pleurosoriopsis` that is
created in the user's working directory. Notice that it at first does not
contain any output. The analysis takes a few minutes to run. When it finishes,
there will be a `ms.pdf` file created that includes all the results of the
analysis as a manuscript. You should be able to verify that it is the same as
the published paper.

Note that the image is rather large (3.89 GB), so if internet resources are limited it may not be feasible for all participants to try the example at once.

- Source code: <https://github.com/joelnitta/pleurosoriopsis>

- Paper: [Ebihara et al. 2019. "Growth Dynamics of the Independent Gametophytes of *Pleurorosiopsis makinoi* (Polypodiaceae)" Bulletin of the National Science Museum Series B (Botany) 45:77-86.](https://www.kahaku.go.jp/research/publication/botany/download/45_2/L_BNMNS_B45-2_77.pdf)

## Seeking Examples

Do you have another example of using Docker in a workflow related to your field? Please [open a lesson issue] or [submit a pull request] to add it to this episode and the extras section of the lesson.
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