deploy-refseq.md

RefSeq in MiGA

In this tutorial, we will create a genomes project including all the representative genomes available in RefSeq using MiGA alone. If you want to explore a more manual approach using bash, see the RefSeq in MiGA using BASH example.

0. Initialize the project

miga new -P RefSeq -t genomes
cd RefSeq

1. Download publicly available genomes

Re-running and updating: If the following code fails at any point, for example due to a network interruption, you can simply re-run it, and it will take it from where it failed.

miga ncbi_get -P . --reference -v -T Archaea

Of course, you can repeat for -T Bacteria to get all prokaryotic genomes.

It is strongly recommended to use an NCBI API Key to increase the number of allowed requests. Once you obtain one, you can pass it as an argument:

miga ncbi_get -P . --reference --api-key ABCD123 -v -T Archaea

Or you can set it globally as an environmental variable before running miga:

export NCBI_API_KEY=ABCD123

2. Launch the daemon

Now that your data is ready, you can fire up the daemon to start processing the data. For additional details, see launching daemons:

miga daemon start -P .