Update docs and code to require loqusdb version >= 2.5 if used

This is may be less of a bug report and more of a support issue. But there are some bugs in this as well which I may add to an other issue.

Since the move to using the CLI for LoqusDB we have not been able to configure it properly. We’ve added this to the config.py:

LOQUSDB_SETTINGS = dict(
    binary_path="/correct/path/to/loqusdb"
)

But at this point:

https://github.com/Clinical-Genomics/scout/blob/750c805cefba3e06ca5737d021d71b69bec694e0/scout/server/blueprints/variant/views.py#L53-L57

current_app.config[“LOQUSDB_SETTINGS”] is not set. So data[“observations”] is not populated. I tried printing the whole dictionary and it is really not there!

However if I add {{config}} anywhere in variant.html, it shows that LOQUSDB_SETTINGS is set according to the values in config.py. Why are the config data different in these two places? Do I need to configure loqusdb somewhere else as well?

[ewels]

Ugh, click and its locale settings 🤦‍♂ I would be careful about writing that py3.7 is a requirement - might be worth checking that it wasn’t to do with creating or changing your environment somehow (as a side effect of updating to 3.7). I’ve seen similar bugs crop up and be fixed with some extremely random behaviour in the past. No tips really apart from trial and error. See this old PR: https://github.com/bioconda/bioconda-recipes/pull/5541 for some previous experience if it helps.

[bjhall]

Just FYI, I solved the locale/encoding problem by updating to Python 3.7. Maybe it should be noted somewhere that python>=3.7 is a requirement for loqusdb if you want the scout integration to work.