Update README.md (#192)

README.md

@@ -5,13 +5,15 @@ Log issues and see general documentation at [dockstore](https://github.com/ga4gh
 Port 80 is exposed over http. This port should not be exposed to the public. A separately [configured load
 balancer](https://github.com/dockstore/dockstore-deploy) is responsible for SSL termination and forwarding traffic to this instance. Previously this repo handled the SSL termination with nginx and LetsEncrypt.
 
+If you are looking for how to run Dockstore locally as a developer, you are probably in the wrong place and should take a look at https://github.com/dockstore/dockstore/blob/develop/docker-compose.yml
+
 ## Prerequisities
 
-1. Tested on Ubuntu 16.04.3 LTS
-1. At least 20GB of disk space, 4GB of RAM, and two CPUs
+1. Tested on Ubuntu 20.04
+1. At least 20GB of disk space, 16GB of RAM, and 4 CPUs
 1. Docker setup following [https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/](https://docs.docker.com/engine/installation/linux/docker-ce/ubuntu/) including the post-installation steps for running without sudo
 1. The running Dockstore website will require ports 80 and 443 by default
-1. A client id and client secret for each of the integrations you wish to setup, github and quay.io as a minimum probably. You will need client ids and secrets for each integration as documented at the [Dockstore Primer](https://wiki.oicr.on.ca/display/SEQWARE/Dockstore+Primer#DockstorePrimer-SettingupDockstoreonyourcomputerfordevelopment(AssumingUbuntu)).
+1. A client id and client secret for each of the integrations you wish to setup, github and quay.io as a minimum probably. You will need client ids and secrets for each integration as documented on the internal [wiki](https://wiki.oicr.on.ca/display/DOC/OAuth+Apps+and+Other+3rd+Party+Registration).
 
 ## Usage
 
@@ -32,59 +34,14 @@ rebuild your docker images without affecting existing running containers
 
 4. After following the instructions in the bootstrap script and starting up the site with `docker-compose`, you can browse to the Dockstore site hosted at port 443 by default. `https://<domain-name>` if you specified https or `http://<domain-name>:443` if you did not. 
 
-5.  Note that the following volumes are created, `composesetup_esdata1` for ephermeral elastic search data, `composesetup_log_volume` for logging, and `composesetup_ui2_content` for storing the built UIs before they are handed off the nginx for service. 
+The current setup relies upon an externally hosted database (currently AWS RDS) and externally hosted search (currently AWS Elasticsearch). 
 
-6. For database backups, you can use a script setup in the cron for the host
-
-```
-@daily 		(echo '['`date`'] Nightly Back-up' && /home/ubuntu/compose_setup/scripts/postgres_backup.sh) 2>&1 | tee -a /home/ubuntu/compose_setup/scripts/ds_backup.log
-```
-
-This relies upon an IAM role for the appropriate S3 bucket. You will also need the AWS cli installed via ` sudo apt-get install awscli`. Note that this may not be readily apparent since a cron has a limited $PATH and it seems easy to accidentally get the awscli installed for specific users. 
-
 ### Loading Up a Database ###
 
-The docker-compose setup uses a mount from the host to keep the postgres database persistent (which is different from elastic search which is not) 
-
-However, this does require a convoluted way to add content to the DB as follows
-
-```
-docker-compose down
-# needed since dropping the schema can still leave some user information behind
-sudo rm -Rf postgres-data/
-nohup docker-compose up --force-recreate --remove-orphans &
-docker cp /tmp/backup.sql <container>:/tmp
-docker exec -ti <container> /bin/bash
-su - postgres
-psql
-DROP SCHEMA public CASCADE;
-CREATE SCHEMA public;
-CREATE USER dockstore WITH password 'dockstore';
-ALTER DATABASE postgres OWNER to dockstore;
-ALTER SCHEMA public OWNER to dockstore;
-\quit
-psql postgres -U dockstore -f  /tmp/backup.sql 
-# exit container (ctrl+d) and then run migration using newly loaded DB
-docker-compose down
-nohup docker-compose up --force-recreate --remove-orphans &
-```
-
+Loading up a database is usually not necessary since AWS RDS is persistent. Refer to https://github.com/dockstore/dockstore-deploy#database-setup 
 
 Note that database migration is run once during the startup process and is controlled via the `DATABASE_GENERATED` variable. Answer `yes` if you are working as a developer and want to start work from scratch from an empty database. Answer `no` if you are working as an administrator and/or wish to start Dockstore from a production or staging copy of the database.
 
-### Modifying the Database ###
-
-If direct modification of the database is required, e.g, a curator needs to modify the value of some row/column that is not accessible via the API, you can use the same steps as above, except for dropping the schema.
-
-This should be exercised with extreme caution, and with someone looking over your shoulder, as you have the potential to unintentionally overwrite or delete data. If you wish to proceed:
-
-```
-# Assuming you copied a file `fix.sql` to the /tmp directory:
-docker cp /tmp/fix.sql <container>:/tmp
-docker exec -ti <container> /bin/bash
-su - postgres
-psql -f  /tmp/fix.sql 
-```
 
 ## Logging Usage