DIG-1555 & DIG-1595: Update deployment documentation

.github/ISSUE_TEMPLATE/deployment-error.md

@@ -7,13 +7,16 @@ assignees: ''
 
 ---
 
-**Operating system**
+## Operating system
 - OS (linux, WSL, OSX darwin, OSX arm)
 
-**Step where failure occurred (make-?)**
+## What version are you deploying
 
-**Are there errors in `tmp/error.txt`?**
+## Step where failure occurred (make-?)
 
-**Are there errors in the docker logs for the affected container(s)?**
+## Are there errors in `tmp/error.txt`?
 
-**Any other information**
+## Are there errors in the central log for the affected container(s)? `tmp/logs/*.log`
+<!-- Please specify which services are affected and copy/paste any relevant logs-->
+
+## Any other information

README.md

@@ -9,65 +9,11 @@ dataflow for genomic data.
 
 ## Installation
 
-CanDIG uses a make-based deployment process, with services containerized in Docker. To deploy CanDIGv2, follow the installation guide in `docs/`:
+CanDIG uses a make-based deployment process, with services containerized in Docker. To deploy CanDIGv2, follow the installation guides in `docs/`:
 
 * [CanDIG Deployment Guide](./docs/install-candig.md)
 
-View additional Makefile options with `make help`.
-
-### `.env` Environment File
-
-You need an `.env` file in the project root directory, which contains a set of global variables that are used as reference to the various parameters, plugins, and config options that operators can modify for testing purposes. This repo contains an example `.env` file in `etc/env/example.env`.
-
-For a basic desktop sandbox setup, the example variable file needs very little (if any) modification.
-
-When deploying CanDIGv2
-using `make`, `.env` is imported by `make` and all uncommented variables are added as environment variables via
-`export`.
-
-Some of the functionality that is controlled through `.env` are:
-
-* operating system flags
-* change docker network, driver, and swarm host
-* modify ports, protocols, and plugins for various services
-* version control and app pinning
-* pre-defined defaults for turnkey deployment
-
-Environment variables defined in the `.env` file can be read in `docker-compose` scripts through the variable substitution operator
-`${VAR}`.
-
-```yaml
-# example compose YAML using variable substitution with default option
-services:
-  consul:
-    image: progrium/consul
-    network_mode: ${DOCKER_MODE}
-...
-```
-### Configuring CanDIG modules
-
-Not all CanDIG modules are required for a minimal installation. The `CANDIG_MODULES` setting defines which modules are included in the deployment.
-
-By default (if you copy the sample file from `etc/env/example.env`) the installation includes the minimal list of modules:
-
-```
-  CANDIG_MODULES=keycloak vault minio postgres redis htsget katsu candig-data-portal query tyk opa federation candig-ingest
-```
-
-Optional modules follow the `#` and include various monitoring components, workflow execution, and some older modules not generally installed.
-
-### Configuring CanDIG modules
-
-Not all CanDIG modules are required for a minimal installation. The `CANDIG_MODULES` setting defines which modules are included in the deployment.
-
-By default (if you copy the sample file from `etc/env/example.env`) the installation includes the minimal list of modules:
-
-```
-  CANDIG_MODULES=keycloak vault minio postgres redis htsget katsu candig-data-portal query tyk opa federation candig-ingest
-```
-
-Optional modules follow the `#` and include various monitoring components, workflow execution, and some older modules not generally installed.
-
+See [Interact with the stack](docs/interact-with-the-stack.md) for a guide to additional options or view all Makefile options with `make help`.
 
 ## Project Structure