(docs): Update READMEs with some development tips and a DAG (#1817)

* Update READMEs with some development tips and an ingest DAG. --------- Co-authored-by: Cornelius Roemer <[email protected]> Co-authored-by: Theo Sanderson <[email protected]>
loculus-project · May 28, 2024 · dc14744 · dc14744
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diff --git a/README.md b/README.md
@@ -4,8 +4,18 @@ Loculus is a software package to power microbial genomial databases.
 
 ## [Visit the Loculus documentation website](https://loculus-project.github.io/loculus/)
 
+## Development
+
 Additional documentation for development is available in each folder's README. This file contains a high-level overview of the project and shared development information that is best kept in one place.
 
+If you would like to develop with a full local loculus instance you need to first:
+
+1. Deploy a local kubernetes instance: [kubernetes](/kubernetes/README.md)
+2. Deploy the backend: [backend](/backend/README.md)
+3. Deploy the frontend/website: [website](/website/README.md)
+
+Note that if you are developing the backend or frontend/website in isolation a full local loculus instance is not required. See the individual READMEs for more information.
+
 ## Architecture
 
 - Backend code is in `backend`, see [`backend/README.md`](/backend/README.md)

diff --git a/backend/README.md b/backend/README.md
@@ -69,6 +69,8 @@ We use Flyway, so that the service can provision an empty/existing DB without an
 
 The service listens, by default, to **port 8079**: <http://localhost:8079/swagger-ui/index.html>.
 
+Note: When using a postgresSQL development platform (e.g. pgAdmin) the hostname is 127.0.0.1 and not localhost - this is defined in the `deploy.py` file.
+
 ### Operating the backend behind a proxy
 
 When running the backend behind a proxy, the proxy needs to set X-Forwarded headers:

diff --git a/ingest/README.md b/ingest/README.md
@@ -4,6 +4,14 @@
 
 The following is a rough overview of the pipeline's steps.
 
+The snakemake DAG can be visualized using [graphviz](https://en.wikipedia.org/wiki/Graphviz):
+
+```bash
+snakemake --dag  | dot -Tpng > dag.png
+```
+
+![snakemake DAG](dag.png)
+
 ### Download data from NCBI virus
 
 Using NCBI `datasets` CLI, download all sequences and corresponding NCBI curated metadata for a configurable taxon. The taxon is specified using the NCBI Taxonomy ID, and includes all child taxa, i.e. dowloading sequences for the Ebola virus taxon ID includes all sequences for more specific Ebola virus (sub)species taxon ids.

diff --git a/ingest/dag.png b/ingest/dag.png
diff --git a/kubernetes/README.md b/kubernetes/README.md
@@ -32,6 +32,9 @@ helm install loculus kubernetes/loculus -f my-values.yaml
 
 Install [k3d](https://k3d.io/v5.6.0/) and [helm](https://helm.sh/).
 
+
+We deploy to kubernetes via the `../deploy.py` script. It requires you to have `pyyaml` and `requests` installed.
+
 ### Setup for local development
 
 #### TLDR