Quickstart

Welcome to Kerblam! This introductory chapter will give you the general overview on Kerblam!: what it does and how it does it.

Kerblam! is a project manager. It helps you write clean, concise data analysis pipelines, and takes care of chores for you.

Every Kerblam! project has a kerblam.toml file in its root. When Kerblam! looks for files, it does it relative to the position of the kerblam.toml file and in specific, pre-determined folders. This helps you keep everything in its place, so that others that are unfamiliar with your project can understand it if they ever need to look at it.

These folders, relative to where the kerblam.toml file is, are:

• ./data/: Where all the project's data is saved. Intermediate data files are specifically saved here.
• ./data/in/: Input data files are saved and should be looked for in here.
• ./data/out/: Output data files are saved and should be looked for in here.
• ./src/: Code you want to be executed should be saved here.
• ./src/pipes/: Makefiles and bash build scripts should be saved here. They have to be written as if they were saved in ./.
• ./src/dockerfiles/: Container build scripts should be saved here.

Any sub-folder of one of these specific folders (with the exception of src/pipes and src/dockerfiles) contains the same type of files as the parent directory. For instance, data/in/fastq is treated as if it contains input data by Kerblam! just as the data/in directory is.

You can configure almost all of these paths in the kerblam.toml file, if you so desire. This is mostly done for compatibility reasons with non-kerblam! projects. New projects that wish to use Kerblam! are strongly encouraged to follow the standard folder structure, however.

The rest of these docs are written as if you are using the standard folder structure. If you are not, don't worry! All Kerblam! commands respect your choices in the kerblam.toml file.

If you want to convert an existing project to use Kerblam!, you can take a look at the kerblam.toml section of the documentation to learn how to configure these paths.

If you follow this standard (or you write proper configuration), you can use Kerblam! to do a bunch of things:

• You can run pipelines written in make or arbitrary shell files in src/pipes/ as if you ran them from the root directory of your project by simply using kerblam run <pipe>;
• You can wrap your pipelines in docker containers by just writing new dockerfiles in src/dockerfiles, with essentially just the installation of the dependencies, letting Kerblam! take care of the rest;
• If you have wrapped up pipelines, you can export them for later execution (or to send them to a reviewer) with kerblam package <pipe> without needing to edit your dockerfiles;
• If you have a package from someone else, you can run it with kerblam replay.
• You can fetch remote data from the internet with kerblam data fetch, see how much disk space your project's data is using with kerblam data and safely cleanup all the files that are not needed to re-run your project with kerblam data clean.
• You can show others your work by packing up the data with kerblam data pack and share the .tar.gz file around.
• And more!

The rest of this tutorial walks you through every feature.

I hope you enjoy Kerblam! and that it makes your projects easier to understand, run and reproduce!

If you like Kerblam!, please consider leaving a star on Github. Thank you for supporting Kerblam!