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CONTRIBUTING.adoc

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Contributing

This guide describes how to submit a new species for the Swedish Reference Genome Portal

In the following examples, we will assume that you (Github user insidethebox) want to add the Yellow boxfish (described as Ostracion cubicum by Linné in 1758) species to the Genome Portal.

Prerequisites

Start by forking the genome-portal repository from your Github account.

Clone the repository to your computer, and create a branch to work on. Name the branch after the scientific name of the species:

git clone [email protected]:insidethebox/genome-portal.git
cd genome-portal
git checkout -b ostracion-cubicum

Reference genome and gene annotation

The first elements we ask you to provide are a reference assembly and a genome annotation.

Create a file named config.yml using the following model:

assembly:
  name: yellow_boxfish_assembly
  displayName: "Yellow boxfish genome assembly"
  # The following URL points to the public repository hosting the assembly
  url: "https://example.com/repository/GCA_255255000.fasta.gz"
  fileName: GCA_255255000.fasta.gz
tracks:
  - name: "Protein coding genes"
    # Ditto
    url: "https://example.com/repository/GCA_255255000.gff.gz"
    fileName: GCA_255255000.gff.gz

Within the genome-portal repository, place this file its own directory under config/, named after the species scientific name:

cd genome-portal
mkdir config/ostracion_cubicum
mv config.yml config/ostracion_cubicum

Commit and push your changes

git commit -am "Base configuration for Ostracion cubicum"
git push origin ostracion-cubicum

Open a pull request

Now to start the onboarding process, create a pull request. (We encourage you to tick the option allowing us to make changes, for the ease of collaboration)

In the pull request description, tell us a few words about yourself and your academic involvement with the proposed species.

That’s it for a start: we will be notified and guide you through the next steps in the pull request discussion.