Once you have wrapped a method using a script and definition, all you need to share your method is a Dockerfile which lists all the dependencies that need to be installed.
We’ll work with the following definition.yml:
#!/usr/bin/env python import dynclipy dataset = dynclipy.main() import pandas as pd import sklearn.decomposition # infer trajectory pca = sklearn.decomposition.PCA() dimred = pca.fit_transform(dataset['expression']) pseudotime = pd.Series( dimred[:, dataset['parameters']['component']-1], index = dataset['expression'].index ) # build trajectory trajectory = dynclipy.wrap_data(cell_ids = dataset['expression'].index) trajectory.add_linear_trajectory(pseudotime = pseudotime) # save output trajectory.write_output(dataset['output'])
Make sure it is executable
Assuming that the definition.yml and run.R are located in current directory, a minimal Dockerfile would look like:
dynverse/dynwrappy is here the base image, which contains the latest version of R, python, dynwrap, dyncli and most tidyverse dependencies. For R methods, you can use the
dynverse/dynwrapr base. While not required, it’s recommended to start from these base images, because dyncli provides an interface to run each method using the docker container from the command line. As discussed before, wrapping is also a lot easier using dynwrap.
For reproducibility, it’s best to specify the tag of the base image. You can find this these tags on dockerhub: https://hub.docker.com/r/dynverse/dynwrapr/tags.
The Dockerfile then copies over the definition.yml and run.py file inside the “code” directory. Typically, you won’t change the locations of these files, simply to maintain consistency with the rest of the method wrappers included in dynmethods.
Finally, we specify the entrypoint, which is the script that will be executed when the docker is run.
Do not specify this entrypoint using
ENTRYPOINT /code/run.R, because this will create issues with specifying command-line arguments.
That’s it! Assuming that you have a functioning docker installation, you can build this container using
This method can now be loaded inside R using dynwrap
If you have dynplot installed, you can also plot the trajectory:
Congratulations! You now have a TI method that can be easily installed anywhere without dependency issues, and that can be included within the whole dynverse pipeline.
So what’s left?
To make a project like this maintainable in the long run, it is important that everytime something is changed, the method is tested to make sure it works fine.
To do this, we first add an example.sh file, which will generate an example dataset that will certainly run without any error with the method. In this case, this example is just the example dataset included in dynwrap.
You can of course provide your own example data here, but make sure it doesn’t take too long to generate, and not too long for the TI method run.
You can also add extra parameters and a fixed seed to the example data, e.g.:
dataset$seed <- 1 and
dataset$parameters <- list(component = 42)
Now run the example script and test it:
To automate the testing (and building) of containers, you’ll have to use continuous integration. We use travis-ci for this, a free service for open-source projects. Because the exact code to use this continuous integration requires some manual steps, we suggest you create an issue at dynmethods so that we can help you further. If you’re really adventurous, you can have a look at some of our .travis.yml files, e.g.: https://github.com/dynverse/ti_paga/blob/master/.travis.yml
Once the continuous integration works, you’re method is ready to be included in dynmethods!