Build

Build

[TOC]

See also

For a complete end-to-end walkthrough covering build, stage, serve, and push, see the Building and Serving Tutorial.

Introduction

Once you’ve installed refgenie, you can use refgenie pull to download pre-built assets without installing any additional software. However, you may need to use the build function for genomes or assets that are not available on the server. You can build assets for any genome for which you can provide the required inputs.

Building assets is a bit more complicated than pulling them. You’ll need to set up 2 things: 1) any inputs required by the asset build recipe; 2) Any software required by the recipe. Below, we’ll walk you through each of these requirements, but first, how can you tell what refgenie can build in the first place?

What assets can refgenie build?

Refgenie now features a flexible asset class and recipe system, allowing users and tool developers to define, share, and manage their own asset types and build methods. Instead of being limited to a fixed set of internally-defined assets, you can now introduce new asset classes and recipes via external YAML or JSON files—without modifying refgenie’s source code. This enables multiple assets of the same class to coexist, supports community-driven innovation, and decouples asset types from recipes for greater workflow flexibility.

Data Channels: Refgenie’s extensibility is powered by data channels—external sources that provide definitions for asset classes and recipes. Data channels enable the community to publish, distribute, and synchronize new types of reference genome assets and build instructions across the refgenie ecosystem. Through data channels, organizations and tool developers can share their custom asset types with the broader community without requiring changes to the core refgenie codebase.

For a detailed overview of this system and how to define or use custom asset types and recipes, see the Flexible Asset Types documentation. To learn more about how data channels work and how to create or use them, see the Data Channels documentation

Recipes require inputs

Each asset requires some inputs, which we classify as assets, files or parameters.

input class	recipe name	command line argument	input type
assets	required_assets	--assets	asset registry path
files	required_files	--files	file/dir path
parameters	required_parametes	--params	string

To view required inputs for an asset, add an -q or --requirements flag to the refgenie build command:

$ refgenie build hg38/bowtie2_index -q

                                                                               Recipes
┏━━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━┓
┃ Name          ┃ Version ┃ Output asset class ┃ Input asset classes                ┃ Input files ┃ Input params                        ┃ Docker image               ┃
┡━━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━┩
│ bowtie2_index │ 0.0.1   │ bowtie2_index      │ • fasta (fasta asset for genome)   │ None        │ • threads (Number of threads to     │ docker.io/databio/refgenie │
│               │         │                    │ default=fasta                      │             │ use) default=1                      │                            │
└───────────────┴─────────┴────────────────────┴────────────────────────────────────┴─────────────┴─────────────────────────────────────┴────────────────────────────┘─────────────────────────────┴─────────────┴─────────────────────────────────────┴────────────────────────────┘

Notice how ‘fasta’ appears under assets and not under files or params. This means to build a bowtie2 index, you do not provide a fasta file as an argument; instead, you must already have a fasta asset managed by refgenie. One advantage of this is that it allows refgenie to keep a record of how you’ve built your assets, so refgenie can remember the link between this bowtie2 asset and the fasta asset, which turns out to be very useful for maintaining provenance of your assets. It also makes it easier to build derived assets like this, because you don’t actually have to pass any additional arguments to build them.

So, you’ll need to build the fasta asset for hg38 genome before building bowtie2_index, but once you have that, building this asset is as simple as typing:

refgenie build hg38/bowtie2_index

For many of the built-in recipes, a pre-existing fasta asset is the only requirement and refgenie will use the correct one by default. However, if you wish to build an asset with a different asset as an input, refgenie provides full flexibility. For instance, you can use fasta:other_tag (non-default tag) or even hg38_cdna/fasta (fasta asset from a different namespace) by adding --assets argument to the refgenie build command, like so:

refgenie build hg38/bowtie2_index --assets fasta=hg38_cdna/fasta

This will build a bowtie2_index asset in hg38 namespace but based on a transcriptome fasta.

Next, here’s an example of an asset that requires an argument, but not a pre-existing asset:

$ refgenie build hg38/refgene_anno -q

┏━━━━━━━━━━━━━━┳━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━┳━━━━━━━━━━━━━━━━━━┓
┃ Name         ┃ Version ┃ Output asset class ┃ Input asset classes ┃ Input files                                                  ┃ Input params ┃ Docker image     ┃
┡━━━━━━━━━━━━━━╇━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━╇━━━━━━━━━━━━━━━━━━┩
│ refgene_anno │ 0.0.1   │ refgene_anno       │ None                │ • refgene (gzipped RefGene database annotation file)         │ None         │ databio/refgenie │
│              │         │                    │                     │ default=None                                                 │              │                  │
└──────────────┴─────────┴────────────────────┴─────────────────────┴──────────────────────────────────────────────────────────────┴──────────────┴──────────────────┘

You’ll need to provide this recipe with a refgene file, like this:

refgenie build hg38/refgene_anno --files refgene=REFGENE_FILE.txt.gz

You can see the example build output.

Recipes require software

If you want to build assets, you’ll need to get the software required by the asset you want to build. You have three choices to get that software: you can either install it natively, use a docker image, or use a bulker manifest.

Install build software natively

Refgenie expects to find in your PATH any tools needed for building a desired asset. You’ll need to follow the instructions for each of these individually. You could find some basic ideas for how to install these programatically in the dockerfile. We discourage this approach because it makes the assets dependent on your particular uncontrolled environment, which is not ideal. As a result, we don’t have great documentation for what is required if you want to use this native approach. As we develop a custom asset system, we’re planning to revamp this to provide more detailed way to see what requirements are for a specific recipe.

Build assets with docker

If you don’t want to install all the software needed to build all these assets (and I don’t blame you), then you can just use docker. Each of our recipes knows about a docker image that has everything it needs. If you have docker installed, you should be able to simply run refgenie build with the -d flag. For example:

refgenie build -d genome/asset ...

This tells refgenie to execute the building in a docker container requested by the particular asset recipe you specify. Docker will automatically pull the image it needs when you call this. If you like, you can build the docker container yourself like this:

git clone https://github.com/databio/refgenie.git
cd refgenie/containers
make refgenie

or pull it directly from dockerhub like this:

docker pull databio/refgenie

Build assets with bulker

For an even more seamless integration of containers with refgenie, learn about bulker, our multi-container environment manager. Here, you’d just need to do this:

pip install bulker

# Next, configure bulker according to your local compute environment

bulker load databio/refgenie:0.7.0
bulker activate databio/refgenie:0.7.0
refgenie build ...

Bulker works on both singularity and docker systems. The bulker docs also contain a more complete tutorial of using bulker and refgenie together.

Staging after building

Once you have built an asset, you can stage it to make it available for serving or pushing to cloud storage. You can do this in a separate step:

refgenie build hg38/bowtie2_index
refgenie stage stage hg38/bowtie2_index

Or combine building and staging in one command with the --stage flag:

refgenie build hg38/bowtie2_index --stage

You can also create push intent records at the same time using --push-to:

refgenie build hg38/bowtie2_index --stage --push-to my-s3-remote

The --push-to flag accepts one or more remote names or IDs. After the build and stage complete, refgenie creates records indicating that these assets should be pushed to the specified remotes. You then run refgenie push to execute the actual upload.

See Stage assets for serving for details on the staging system and Configure remote storage for setting up remotes.

Versioning the assets

Refgenie supports tags to facilitate management of multiple “versions” of the same asset. Simply add a :your_asset_name appendix to the asset registry path in the refgenie build command and the created asset will be tagged:

refgenie build hg38/bowtie2_index:my_asset_name