feat: documentation for new instance deployment (#4)

- Allow running in {docker,podman}-compose
- Add docs and initial tutorial for deploying a new instance with
example datasets
- Bring in the search index as additional Docker container in compose
- Use pixi for dep management
- Trigger metadata update for mongodb outside image creation, use only
one mongodb container in compose
- Add sentry for monitoring (opt-in)
- Flask app checks for errors from the search index
- Use docker links to connect to mongodb and search index by container
name
- Update mgnify component to (unreleased) one containing better sequence
parsing:
EBI-Metagenomics/mgnify-sourmash-component#4
- Update sourmash to 0.13.0 (rust) and use new APIs for revindex
- Add snakemake rules for building search index from example datasets

---------

Co-authored-by: Tessa Pierce Ward <[email protected]>

.dockerignore

@@ -0,0 +1,12 @@
+# ignore everything
+**
+
+# except
+!crates/
+!assets/
+!flake.nix
+!flake.lock
+!Cargo.toml
+!Cargo.lock
+!pixi.toml
+!pixi.lock

.envrc

@@ -1,3 +1,6 @@
-use flake
-
 dotenv .env
+
+PATH=~/.pixi/bin:$PATH
+
+watch_file pixi.lock
+eval "$(pixi shell-hook)"

.gitignore

@@ -5,3 +5,8 @@ buildmongo/bqKey.json
 sandbox/
 result
 docs/_build
+prod.env
+mongodb/
+# pixi environments
+.pixi
+