agr_amplify_jbrowse2

An AWS Amplify oriented repo for building AGR's JBrowse 2

Building for a new release

tldr;

The stage instance of the Alliance JBrowse instance is built at AWS Amplify from the stage branch of this repo and and the production instance of JBrowse is built from the main branch. Typically, the only thing that needs to happen to prep for a new release is to update the Alliance release version and the WormBase release version in the various URLs that refer their data sets (outlined below).

Most MODs' data

Building a new JBrowse instance for a release is a little chaotic. The GFF and VCF processing are described in the agr_jbrowse_gff and agr_jbrowse_vcf repos, and the basics of preparing the config.json are covered there as well, but there isn't a fixed method of keeping the MOD-specific tracks up to date. The templates directory in this repo holds the ad-hoc scripts and results that I used to convert JBrowse configurations at the various MODs to JBrowse 2 configuration segments.

WormBase

All of the MODs but WormBase update their data in place, so barring the addition or deletion of tracks to the MOD JBrowse instance, these tracks should stay up to date "on their own."

WormBase, on the other hand, has the WormBase release version in the url of the track data. The easiest way to create an update of the Alliance JBrowse instance WormBase tracks is to run a global search and replace, like with this Perl one-liner:

perl -pi -e 's/WS289/WS292/' config.json

Of course, the only things you need to know what the old and new WormBase releases are.

Alliance-specific data

The other thing that needs to be updated in the JBrowse configuration is the Alliance release number. A similar one-liner can take care of this:

perl -pi -e 's!/7\.2\./0/!/7.3.0/!' config.json

After making these changes, a commit to the stage branch will trigger a rebuild of the stage JBrowse instance.

Updating the version of JBrowse

It isn't strictly necessary to update the version of JBrowse that the Alliance website is running, but of course it's nice to have new functionality and bug fixes. Fortunately updating the JBrowse version is fairly strightforward. All that is needed is the JBrowse commandline tool, which can be obtained from npm:

npm install -g @jbrowse/cli

For more information about the JBrowse CLI, see the documentation page. Before running the JBrowse CLI to upgrade, it's a good idea to clean out the javascript directory, since there are many files there and an upgrade will deprecate some of them, update some and add new ones. After a few upgrade cycles, the directory will have lots of javascript files that are no longer used. Since these files are under git control, we need to git rm them:

git rm static/js/*

Then we can run the update and add the new files to the repo:

jbrowse upgrade
git add --all
git commit
git push

and of course, after the push to the stage branch, the JBrowse instance on the stage site will rebuild, and you should definitely go make sure it's working as expected!