diff --git a/_episodes/docker-image-examples.md b/_episodes/docker-image-examples.md index f75bf20a9..bc3fe2595 100644 --- a/_episodes/docker-image-examples.md +++ b/_episodes/docker-image-examples.md @@ -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: + +- 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.