Genus centric JBrowse2 hosting

Currently, we are using a shared JBrowse2 setup hosted on a production VM at NCGR (jbrowse2-legumeinfo). The shared setup in theory means that customizations like plugins can be managed for all our separate genus sites (each genus site's Jbrowse2 is really just its Jbrowse2 config file).

The legumista account has pip installed lis-autocontent into its userspace and has ownership of the JBrowse2 related folders so it is most convenient to sudo -s -u legumista for using the lis-autocontent functions. NOTE: the pypi version tends to lag behind development, so until we get a better release management strategy, use the version you get from . ~legumista/lis_autocontent_env/bin/activate Latest (currently) jbrowse2 code is unzipped into a version-specific folder: /var/www/html/jbrowse-web-v2.3.4 within that folder, make a subfolder to contain the config for your genus, e.g. vigna then inside the vigna folder, you can construct a config based on datastore contents as:

lis-autocontent populate-jbrowse2 --jbrowse_url https://vigna.legumeinfo.org/tools/jbrowse2/ --jbrowse_out . --taxa_list vigna.yml

Note that you'll want to have an updated clone of the datastore-metadata repo accessible (ie in the current folder if invoked as above)