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Build assets


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?

At the moment the building functionality is under rapid development and may change in the future. While refgenie is totally flexible with respect to genome, it is more restricted in terms of what assets it can build. We are planning to allow users to specify their own recipes for arbitrary assets, but at the moment, refgenie can only build a handful of assets for which we have already created building recipes. If you type refgenie list, you'll get a list of all the assets you can build with refgenie (under recipes). You can also browse the list of available assets here. If you need refgenie to manage an asset not in this list, you can either 1) wait for our pending implementation of custom recipes, or 2) add custom assets, which you would build separately and then use refgenie just to manage them as recipes define reasonable defaults, which rarely require changing.

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

'bowtie2_index' recipe requirements:
- assets:
    fasta (fasta asset for genome); default: fasta

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

'refgene_anno' recipe requirements:
- files:
    refgene (gzipped RefGene database annotation file)

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
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.

Versioning the assets

Refgenie supports tags to facilitate management of multiple "versions" of the same asset. Simply add a :your_tag_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_tag

You can also learn more about tagging refgenie assets.

Build assets concurrently

Starting with refgenie 0.11.1, the assets may be built following the MapReduce programming model, whereby the refgenie build process is split into two tasks: building assets (Map procedure) and gathering asset metadata (Reduce procedure). These tasks can be launched with --map and --reduce flags, respectively.

Map procedure builds the assets as usual, but stores the metadata in a separate, newly created genome configuration file. This avoids any conflicts in concurrent asset builds.

Reduce procedure finds the genome configuration files produced in the Map step, updates the main genome configuration file with their contents and removes them.

# run multiple, possibly hundreds of concurrent builds
refgenie build genome/asset --map
refgenie build genome1/asset --map
refgenie build genome1/asset2 --map

# combine built assets metadata in the main config
refgenie build --reduce

Refgenie does not account for assets dependancy. Therefore, for best results, consider the following order of building assets:

  1. refgenie build --map all fasta assets to establish genome namespaces
  2. Wait until jobs are completed, call refgenie build --reduce
  3. refgenie build --map all other top-level assets, e.g. fasta_txome, gencode_gtf
  4. Wait until jobs are completed, call refgenie build --reduce
  5. refgenie build --map all derived assets, e.g. bowtie2_index, bwa_index
  6. Wait until jobs are completed, call refgenie build --reduce

Alternatively, the assets can be automatically retrieved from refgenieserver, if they exist.

Automatically pull parents of derived assets

Starting with refgenie 0.11.1, refgenie build command can automatically pull the default parent assets if required but not provided. This feature can be toggled on with --pull-parents option.

For example you can build a bowtie2_index asset right after refgenie initialization, like so:

export REFGENIE=refgenie_config.yaml
refgenie init -c $REFGENIE
refgenie build hg38/bowtie2_index --pull-parents

The refgenie build --pull-parents command will first try to download the default parent for hg38/bowtie2_index asset, which is hg38/fasta, and build the hg38/bowtie2_index asset right after.

In case the default asset parents are not available on any of the servers you have refgneie subscribed to, the build will not start and exit with 1.