AmpliconRepository.org

Authors: Ted Liefeld, Jens Luebeck, Edwin Huang, Forrest Kim, Thorin Tabor, Michael Chan, Dhruv Khatri, Kyra Fetter, Gino Prasad, Rohil Ahuja, Rishaan Kenkre, Tushar Agashe, Devika Torvi, Madalina Giurgiu, Vineet Bafna

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This is the main repository for the AmpliconRepository website. The documentation below provides intsructions on deploying the site locally, for development purposes.

• How to install the development environment for AmpliconRepository
• How to set up your development environment using docker compose
• Testing datasets
• Pushing changes to GitHub and merging PRs
• Using the development server
• Logging in as admin
• Running the automated tests
• REST API v1
• How to deploy and update the production server for AmpliconRepository

There are two options for running the server locally:

Option A: Manually install modules and configure the environment step-by-step.

Option B: Use Docker to deploy the server and its environment on your system.

Option A - install the development environment for AmpliconRepository:

Requirements

• Python Virtual Environment (3.8 or higher)

1. Clone the repository from GitHub

• Clone repo using https, ssh, or GitHub Desktop to your local machine

2. Set up the virtual environment and install packages:

• In a terminal window, move to the cloned GitHub repo
• Go to the AmpliconRepository top level directory (should see requirements.txt)

Option A: Using python's environment manager

• Create a new Python virtual environment:

python -m venv ampliconenv

• Activate the new environment (you need to do this everytime before running the server):

source ampliconenv/bin/activate

• Install required packages

pip install -r requirements.txt

Option B: Using conda's environment manager

• Create a new Conda environment

conda create -n ampliconenv "python>=3.8,<3.13"

• To activate

conda activate ampliconenv

• Install pip to that environment

conda install pip -n ampliconenv

• Install required packages

~/[anaconda3/miniconda3]/envs/ampliconenv/bin/pip install -r requirements.txt

3. Set up MongoDB locally (for development)

• Install MongoDB

  • In Ubuntu this can be done with sudo apt install mongodb-server-core

    • For newer versions of Ubuntu (e.g. 22.04+), follow the instructions here: https://www.fosstechnix.com/how-to-install-mongodb-on-ubuntu-22-04-lts/

  • In macOS this can be done with

    git config --global init.defaultBranch main

    brew tap mongodb/brew

    brew install mongodb-community@6.0

  • If the package is not found you may need to follow the directions here.

• If you don't have a database location set up, set up a location:

mkdir -p ~/data/db/

• In a terminal window or tab with the ampliconenv environment active, run MongoDB locally:

mongod --dbpath ~/data/db or mongod --dbpath <DB_PATH>

3a. View MongoDB data in MongoDB Compass

• Download MongoDB Compass: https://www.mongodb.com/docs/compass/current/install/#download-and-install-compass
• Open the MongoDB Compass app after starting MongoDB locally
• Connect to your local instance of MongoDB:

URI: mongodb://localhost:27017

• Relevant data will be located in /AmpliconRepository/projects/
• You can periodically clear your local deployment mongodb files using Compass so that your disk does not fill up.
• Run export DB_URI_SECRET='mongodb://localhost:27017' in your terminal to set the environment variable for your local database.
  • So that this is active every time, you can add the command above to your ~/.bashrc file
• Note that the latest version of Compass (1.34.2) won't work with our older DB version. You can get an old compass for mac at https://downloads.mongodb.com/compass/mongodb-compass-1.28.4-darwin-x64.dmg

3b. Cleaning your local DB

Periodically, local development uploads and test projects can make MongoDB's GridFS storage very large. Start with read-only reports:

source caper/config.sh && python purge-local-db.py --gridfs-usage-by-type --limit 25

source caper/config.sh && python purge-local-db.py --gridfs-usage-by-project --limit 25

source caper/config.sh && python purge-local-db.py --tarfile-report --limit 25

The recommended cleanup is two-stage. First remove unreachable project documents and the GridFS/S3/tmp files attached to those documents:

source caper/config.sh && cd caper && python ../cleanup_orphaned_projects.py --dry-run

source caper/config.sh && cd caper && python ../cleanup_orphaned_projects.py

Then remove remaining GridFS blobs that are not referenced by reachable project documents:

source caper/config.sh && python purge-local-db.py --smart-gridfs

source caper/config.sh && python purge-local-db.py --smart-gridfs --execute

purge-local-db.py is dry-run by default; destructive actions require --execute. A full local project/GridFS wipe is still available, but must be requested explicitly:

source caper/config.sh && python purge-local-db.py --all-project-data --execute

MongoDB/WiredTiger may reuse freed space internally instead of immediately shrinking ~/data/db. To return space to the OS after a large cleanup, use a compact/repair operation or dump and restore the local database into a fresh dbpath.

4. Neo4j Download Instructions

Docker

the easiest way... edit the path at the end to the local drive you want it to use

docker run -d --name neo4j -p 7474:7474 -p 7687:7687 --env NEO4J_AUTH=neo4j/$NEO4J_PASSWORD_SECRET -v /home/ubuntu/AmpliconRepository-dev/neo4j neo4j

macOS

Download and unzip the tar file:
curl -O -C - http://dist.neo4j.org/neo4j-community-5.12.0-unix.tar.gz
tar -xvzf neo4j-community-5.12.0-unix.tar.gz

Start neo4j with the console command:
cd neo4j-community-5.12.0
bin/neo4j console

Go to http://localhost:7474/browser/ and change the auth settings. By default, both user and password are 'neo4j'. Keep user as 'neo4j' and change password to 'password'.

The environment is now set up. Ensure that neo4j is running before querying the graph.

Alternatively, go to https://neo4j.com/deployment-center/, then download the rpm file for the latest Community Edition under the section titled 'Graph Database Self-Managed'. Further instructions are available upon clicking Download. Note that this method has not been tested by our team.

Ubuntu (or Windows via WSL/WSL2)

Please follow this documentation to set up the latest version of Neo4j Community Edition

In brief, you can do

wget -O - https://debian.neo4j.com/neotechnology.gpg.key | sudo apt-key add -
echo 'deb https://debian.neo4j.com stable latest' | sudo tee /etc/apt/sources.list.d/neo4j.list
sudo apt-get update
sudo apt-get install neo4j

Register for an account at Neo4j Aura Console

Then launch it by running

sudo neo4j start

Visit http://localhost:7474 and login with neo4j as both the user and password. You will be prompted to set a password for future use. You must set the updated password to the value in your config.sh file (value of NEO4J_PASSWORD_SECRET)

For shutdown at the end of your session, you can do sudo neo4j stop

5. Set up secret keys for OAuth2 and other environment variables

• Make sure you have the config.sh file from another developer (this contains secret key information)
• Run the command to initialize variables (from the top-level repo directory): source caper/config.sh

For local deployments, you will need to ensure that the following two variables are set to FALSE, as shown below

export S3_STATIC_FILES=FALSE
export S3_FILE_DOWNLOADS='FALSE'

IMPORTANT: After recieving your config.sh, please ensure you do not upload it to Github or make it available publicly anywhere.

6. Run development server (Django)

• Open a terminal window or tab with the ampliconenv environment active
• Move to the caper/ folder (should see manage.py)
• Run the server locally:

python manage.py runserver

• Open the application on a web browser (recommend using a private/incognito window for faster development):

https://localhost:8000

• Troublshooting tip: If you face an error that says port 8000 is already in use, you can kill all tasks using that port by doing sudo fuser -k 8000/tcp

Option B - Local deployment with Docker:

These steps guide users on how to set up their development environment using Docker and docker compose as an alternative to python or conda-based package management and installation. This is the simplest way to locally deploy the server for new users.

Important: You first need to install docker>=20.10 on your machine.

To test the installation of Docker please do:

# check version: e.g. Docker version 20.10.8, build 3967b7d
docker --version

# check if compose module is present
docker compose --help

# check docker engine installation
sudo docker run hello-world

Quickstart

Build and run your development webserver and mongo db using docker:

cd AmpliconRepository
# place config.sh in caper/, and place .env in current dir
# change UID and GID in .env to match the host configuration
# create all folders which you want to expose to the container
mkdir -p logs tmp .aws .git
docker compose -f docker-compose-dev.yml build --no-cache --progress=plain
docker compose -f docker-compose-dev.yml up -d
# then visit http://localhost:8000/ in your web browser
# once finished, to shutdown:
docker compose -f docker-compose-dev.yml down

Complete steps

i. Start your docker daemon and make sure is running:

# for linux
sudo systemctl start docker
docker --help
docker compose --help

# or alternatively start manually from interface (macos or windows)

ii. Clone the repository (skip this if you have already done this):

git clone https://github.com/AmpliconSuite/AmpliconRepository.git

iii. Build a local Docker image:

This command will create a Docker image genepattern/amplicon-repo:dev-test with your environment, all dependencies and application code you need to run the webserver. Additionally, this command will pull a mongo:4 image for the test database.

First, obtain the secret files .env and config.sh from another developer. Do not share these files with others outside the project. Do not upload them anywhere. Keep them private.

Next, Place .env under AmpliconRepository/ and config.sh under AmpliconRepository/caper/.

You should see these required files:

• docker-compose-dev.yml
• Dockerfile
• .env
• requirements.txt
• caper/config.sh

cd AmpliconRepository
docker compose -f docker-compose-dev.yml build --progress=plain --no-cache

iv. Run webserver and mongo db instances:

This command will:

• create two containers, one for the webserver (amplicon-dev) and one for the mongo database (ampliconrepository_mongodb_1)
• will use .env to configure all environment variables used by the webserver and mongodb
• will start the webserver on localhost:8000
• will start a mongodb instance listening on port 27017
• will mount a volume with your source code -v ${PWD}:/srv/:rw

# create all folders exposed to container
mkdir -p logs tmp .aws .git
# start container using the host UID and GID (change in .env)
docker compose -f docker-compose-dev.yml up -d
#[+] Running 2/2
# ⠿ Container ampliconrepository-mongodb-1  Started                                                                                                                           0.3s
# ⠿ Container amplicon-dev                  Started                                                                                                                           1.1s

To check if your containers are running do:

docker ps

and you should see something like below:

# CONTAINER ID   IMAGE                                COMMAND                   CREATED         STATUS              PORTS                      NAMES
# 311a560ec20a   genepattern/amplicon-repo:dev   "/bin/sh -c 'echo \"H…"   3 minutes ago   Up About a minute   0.0.0.0:8000->8000/tcp     amplicon-dev
# deaa521621f1   mongo:4                              "docker-entrypoint.s…"    4 days ago      Up About a minute   0.0.0.0:27017->27017/tcp   ampliconrepository_mongodb_1

To view the site locally, visit http://localhost:8000/ in your web browser.

v. Stop webserver and mongodb

To stop the webserver and mongodb service:

docker compose -f docker-compose-dev.yml down
#[+] Running 3/2
# ⠿ Container amplicon-dev                  Removed                                                                                                                          10.3s
# ⠿ Container ampliconrepository-mongodb-1  Removed                                                                                                                           0.3s
# ⠿ Network ampliconrepository_default      Removed                                                                                                                           0.0s

vi. Check environment configuration of your docker-compose

Before you build your image you can check if the config.sh is set correctly by doing:

docker compose -f docker-compose-dev.yml config

This command will show you the docker-compose-dev.yml customized with your environment variables.

vii. Check environment variables for running container

You can check the environment variables which your running container uses:

docker inspect -f \
   '{{range $index, $value := .Config.Env}} {{$value}}{{println}}{{end}}' \
   container_id

viii. Debug

• Run docker ps and check if the port mapping is correct, i.e. you should see 0.0.0.0:8000->8000=host_localip:host_port->docker_port
• Port mapping annotation for docker run -p 8000:8000 ...=HOST:DOCKER
• For local development you need to use host port 8000 to be able to use the Google Authentication in the App
• Set AMPLICON_ENV_PORT if you want to use another port on the host machine, then rebuild the docker image.
• If you get the error permission denied/read only database please set the read-write permissions on your local machine to 777 for the following sudo chmod 777 logs/ tmp/ .aws/ caper/caper.sqlite3 -R
• If you have an older version of docker docker compose may not be available and you will need to install docker-compose and use that, replacing docker compose with docker-compose.
• Error: unix /var/run/docker.sock: connect: permission denied -> see
• If you need to run as a non-root user (rare), please set UID and GID in your .env file to match the host UID GID, or run as so: env UID=${UID} GID=${GID} docker compose -f docker-compose-dev.yml up
• Make sure all folders which are mounted as volumes at runtime are created upfront (below for development): cd AmpliconRepository; mkdir -p logs tmp .aws .git
• My local mongodb instance is not running or you get ampliconrepository-mongodb-1 exited with code 14? Try do cd AmpliconRepository; rm -rf data and restart using docker-compose

Testing datasets

These datasets are ready to upload to the site for testing purposes.

Pushing changes to GitHub and merging PRs

• Work on branches and open pull requests to merge changes into main.
• Please ensure that you do not commit caper.sqlite3 along with your other changes.
• PR reviewers, please check that caper.sqlite3 is not among the changed files in a PR.
• When merging a PR, please do the following steps:
  • pull the branch in question and load in local deployment
  • at minimum, test the following pages to see if everything looks right:
    • home page
    • CCLE project page
    • load a random sample in CCLE

Using the development server

• Please see the wiki page on using the development server.

Logging in as admin

• Please see the wiki page on admin login.

Running the automated tests

The test suite is organized into several tiers by speed and prerequisites, all driven by pytest from the repository root.

Marker	Description	Prerequisites
integration	Unit-style tests against live MongoDB; fast (< 5 s each)	MongoDB running
slow	Full aggregation pipeline per test (several minutes each)	MongoDB + AmpliconSuiteAggregator
functional	End-to-end view tests that depend on pre-loaded datasets	Everything above
browser	Playwright browser tests; require a running dev server	Everything above + dev server

Prerequisites

The same environment you use to run the development server is required:

1. Virtual environment active — activate whichever environment you used during setup:

   source ampliconenv/bin/activate   # python venv
   # or
   conda activate ampliconenv        # conda

2. Install the test runner (one-time, if not already present):

   pip install pytest
   # For browser tests only:
   pip install pytest-playwright && playwright install chromium

3. MongoDB running locally — the tests write to the caper-dev database on localhost:27017:

   mongod --dbpath ~/data/db

4. Environment variables loaded — source config.sh from the caper/ directory:

   source caper/config.sh

   The tests read caper/config.env automatically, but config.sh must have been sourced at least once in the current shell so that shell-level exports are present.

5. AmpliconSuiteAggregator available (for slow and functional tests only) — confirm AGGREGATOR_DEV_PATH in config.sh points to a valid aggregator installation. Tests that use sample-name remapping require v6 or later.

6. Test datasets present — place the following files in test_data/:

   • one_amprepo_sample.tar.gz + one_amprepo_sample.xlsx — 1 sample, hg19 (tracked in git)
   • Contino_unagg_040423.tar.gz — 9 samples, hg38 (download from the shared Google Drive)
   • two_hg38_samples_no_ecdna.tar.gz — 2 hg38 samples, no ecDNA (Google Drive)

   The testing datasets are available on Google Drive.

Running the tests

All commands are run from the repository root (where pytest.ini lives).

Fast integration tests only (no aggregation; safe to run any time):

pytest -m "integration and not slow and not functional and not browser" -v

Full integration + functional tests (requires AmpliconSuiteAggregator; ~10 min):

pytest -m "integration and not browser" -v

End-to-end project lifecycle (slow, creates and aggregates real projects):

pytest -m "slow and integration" -v

Browser tests (requires a running dev server on port 8000):

# Terminal 1: start the dev server — must be from THIS repository's caper/ directory
cd caper && python manage.py runserver

# Terminal 2: run browser tests
pytest -m browser --base-url http://localhost:8000 -v

Important: The dev server and the pytest process share a SQLite database (caper/caper.sqlite3). Two tests — test_authenticated_user_sees_create_form and test_email_password_login_form_works — inject test users and sessions directly into that database. If the server is started from a different repository clone those tests will skip automatically with a diagnostic message rather than fail.

Expected output for fast integration tests with a correctly configured environment:

tests/test_api.py::test_background_task_status_returns_200         PASSED
tests/test_error_handling.py::test_create_project_without_file     PASSED
tests/test_error_handling.py::test_project_page_nonexistent_id     PASSED
tests/test_error_handling.py::test_download_nonexistent_project    PASSED

Continuous Integration

Pushes and pull requests to main automatically run the fast integration tests via GitHub Actions (.github/workflows/tests.yml). The workflow spins up a MongoDB 6 service container and runs pytest -m "integration and not slow and not functional and not browser".

Slow, functional, and browser tests are excluded from CI because they require AmpliconSuiteAggregator, large test datasets, and a running dev server.

Cleanup

Each test removes all artifacts it created — MongoDB documents, tmp/ directories, and S3 objects — in a finally block, so cleanup happens even when a test fails.

---

REST API v1

AmpliconRepository exposes a read-oriented REST API that lets you list projects, fetch sample metadata, and download project archives — all without a browser.

Authentication

Public projects are accessible without any credentials. Private projects require an API token.

Getting a token

1. Log in to ampliconrepository.org (Google, Globus, or username/password).
2. Go to your Profile page.
3. Under Developer API Token, click Generate / Regenerate Token.
4. Copy the token immediately — it is shown only once.

Pass the token on every request:

-H "Authorization: Token <your-token>"

Tokens can be revoked at any time from the Profile page.

Endpoints

All endpoints are under https://ampliconrepository.org/api/v1/.

---

List projects

GET /api/v1/projects/

Returns all projects visible to the caller. Without a token, only public projects are returned. With a token, private projects where you are a project member are also included.

Optional query parameter

Parameter	Description
name	Case-insensitive substring filter on project name

Example

# All public projects
curl https://ampliconrepository.org/api/v1/projects/

# Your public and private projects
curl https://ampliconrepository.org/api/v1/projects/ \
     -H "Authorization: Token <your-token>"

# Filter by name
curl "https://ampliconrepository.org/api/v1/projects/?name=CCLE" \
     -H "Authorization: Token <your-token>"

Response — JSON array of project objects:

[
  {
    "id": "64a1b2c3d4e5f6a7b8c9d0e1",
    "project_name": "CCLE_2023",
    "description": "Cancer Cell Line Encyclopedia amplicon calls",
    "sample_count": 542,
    "visibility": "public",
    "date": "2023-09-15",
    "publication_link": "https://doi.org/...",
    "creator": "jsmith",
    "reference_genome": "hg38",
    "AA_version": "1.3",
    "AC_version": "1.2",
    "oncogenes": ["MYC", "EGFR"],
    "classifications": ["BFB", "ecDNA"]
  }
]

---

Project detail

GET /api/v1/projects/<id>/

Returns metadata for a single project. Returns 404 if the project does not exist; returns 401 if the project is private and no valid token is supplied.

Example

curl https://ampliconrepository.org/api/v1/projects/64a1b2c3d4e5f6a7b8c9d0e1/ \
     -H "Authorization: Token <your-token>"

Response fields are the same as the list endpoint.

---

Sample listing

GET /api/v1/projects/<id>/samples/

Returns per-sample metadata for every sample in the project. GridFS file-ID fields (Features, Sample_metadata_JSON, Sample_files_JSON) are stripped from the response.

Example

curl https://ampliconrepository.org/api/v1/projects/64a1b2c3d4e5f6a7b8c9d0e1/samples/ \
     -H "Authorization: Token <your-token>"

Response — JSON array of sample objects:

[
  {
    "run": "run1",
    "Sample_name": "GBM39",
    "Cancer_type": "GBM",
    "AA_amplicon_number": 1,
    "Classification": "ecDNA"
  }
]

---

Download project archive

GET /api/v1/projects/<id>/download/

Downloads the project .tar.gz archive.

• S3-backed deployments — returns HTTP 302 to a time-limited presigned URL (valid 10 minutes).
• Local-storage deployments — streams the file directly.

Use curl -L to follow the redirect automatically.

Example

curl -L -O https://ampliconrepository.org/api/v1/projects/64a1b2c3d4e5f6a7b8c9d0e1/download/ \
     -H "Authorization: Token <your-token>"

---

Batch download URL resolution

POST /api/v1/projects/download/
Content-Type: application/json

Resolve a list of project IDs to their individual download URLs in one call. Useful when downloading many projects programmatically — fetch the URL list, then download each archive in a loop.

Projects that do not exist, have no archive, or are inaccessible to the caller appear in skipped rather than raising an error.

Request body

{"ids": ["64a1b2c3d4e5f6a7b8c9d0e1", "64a1b2c3d4e5f6a7b8c9d0e2"]}

Example

curl -X POST https://ampliconrepository.org/api/v1/projects/download/ \
     -H "Authorization: Token <your-token>" \
     -H "Content-Type: application/json" \
     -d '{"ids": ["64a1b2c3d4e5f6a7b8c9d0e1", "64a1b2c3d4e5f6a7b8c9d0e2"]}'

Response

{
  "downloads": [
    {
      "id": "64a1b2c3d4e5f6a7b8c9d0e1",
      "project_name": "CCLE_2023",
      "download_url": "https://ampliconrepository.org/api/v1/projects/64a1b2c3d4e5f6a7b8c9d0e1/download/"
    }
  ],
  "skipped": ["64a1b2c3d4e5f6a7b8c9d0e2"]
}

Then download each archive:

# Download all resolved archives
curl -X POST https://ampliconrepository.org/api/v1/projects/download/ \
     -H "Authorization: Token $TOKEN" \
     -H "Content-Type: application/json" \
     -d '{"ids": ["id1", "id2", "id3"]}' \
  | python3 -c "
import json, sys, subprocess
for entry in json.load(sys.stdin)['downloads']:
    subprocess.run(['curl', '-L', '-O', entry['download_url'],
                    '-H', f'Authorization: Token $TOKEN'])
"

HTTP status codes

Code	Meaning
200	Success
400	Bad request (e.g. ids is not a JSON array)
401	Missing or invalid token, or project is private
404	Project or archive not found
503	Download temporarily unavailable (storage error)

---

How to deploy and update the production server for AmpliconRepository

The server is currently running on an EC2 instance through Docker. The ports active on HTTP and HTTPS through AWS Load Balancer. There are two main scripts to start and stop the server.

Note: While we provide a Dockerfile, local deployment of the site using the docker will only properly work on AWS. Local deployment should be done with a local install using the steps above.

0. Setting up a new server on AWS EC2

This section covers provisioning a fresh EC2 instance. The app container is built on the host and is not published to any registry — it must be built locally. Source code is mounted into the running container at runtime, so routine code updates do not require a container rebuild; only changes to requirements.txt or the Dockerfile do.

i. Provision the EC2 instance

• AMI: Ubuntu Server 22.04 LTS
• Instance type: choose based on expected load (t3.medium or larger recommended)
• Security group: open inbound ports for SSH (22), HTTP (80), HTTPS (443), and the app port defined by AMPLICON_ENV_PORT in config.sh; Neo4j ports 7474 and 7687 should be restricted to internal access only
• After the instance is running, register it with the appropriate AWS Application Load Balancer target group:
  • Production: ampliconrepo-https
  • Dev: dev-ampliconrepository-org

ii. Install Docker

SSH into the new instance and install Docker Engine:

sudo apt-get update
sudo apt-get install -y ca-certificates curl gnupg
sudo install -m 0755 -d /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/ubuntu/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg
sudo chmod a+r /etc/apt/keyrings/docker.gpg
echo "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] \
  https://download.docker.com/linux/ubuntu $(. /etc/os-release && echo "$VERSION_CODENAME") stable" \
  | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null
sudo apt-get update
sudo apt-get install -y docker-ce docker-ce-cli containerd.io
sudo usermod -aG docker ubuntu
# Log out and back in for the group membership to take effect

iii. Create the two working checkouts

Two separate git checkouts are maintained to allow container rebuilds without interrupting a running server:

• Running server: /home/ubuntu/AmpliconRepository-<ENV> — the live checkout whose source is mounted directly into the running container (dev or prod)
• Build directory: /home/ubuntu/ampRepo_for_docker_build/AmpliconRepository — used only for docker build; changes here do not affect the running server

# Running server checkout (use AmpliconRepository-dev for the dev environment)
git clone https://github.com/AmpliconSuite/AmpliconRepository.git /home/ubuntu/AmpliconRepository-prod

# Build-only checkout
mkdir -p /home/ubuntu/ampRepo_for_docker_build
git clone https://github.com/AmpliconSuite/AmpliconRepository.git /home/ubuntu/ampRepo_for_docker_build/AmpliconRepository

iv. Create required directories and place config.sh

cd /home/ubuntu/AmpliconRepository-prod   # or AmpliconRepository-dev
mkdir -p logs tmp neo4j/conf neo4j/data

Place config.sh at caper/config.sh inside the running-server checkout. The checkout root is mounted as /srv/ inside the container, so the file will be read from /srv/caper/config.sh at runtime. config.sh contains all environment-specific secrets and settings — database connection strings, OAuth keys, S3 bucket names, and so on. Obtain it from another team member. Do not commit it to git.

MongoDB connectivity uses the existing DocumentDB cluster; the connection string is provided via the DB_URI_SECRET variable in config.sh.

v. Configure AWS credentials

The container mounts /home/ubuntu/.aws so that the application can reach S3. Use one of:

• IAM instance role (preferred for EC2): attach a role with the required S3 permissions to the instance — no credential file is needed
• Access keys: place credentials in /home/ubuntu/.aws/credentials in the standard AWS shared credentials format

vi. Build the Docker image

Build from the build-only checkout so the running server is not affected. The image packages the Python virtual environment and system dependencies; source code is supplied at runtime via volume mount and does not need to be re-baked on every code change.

cd /home/ubuntu/ampRepo_for_docker_build/AmpliconRepository/caper
source caper/config.sh          # sets AMPLICON_ENV and other variables
docker build -t genepattern/amplicon-repo:${AMPLICON_ENV} .

vii. Start Neo4j

Neo4j runs as a Docker container. Run the start script from the running-server checkout root (where caper/config.sh is visible at the relative path the script expects):

cd /home/ubuntu/AmpliconRepository-prod   # or AmpliconRepository-dev
./start-neo4j-container.sh

Neo4j data and configuration are persisted in neo4j/data/ and neo4j/conf/ under the checkout root. To stop Neo4j:

./stop-neo4j-container.sh

viii. Start the application server

cd /home/ubuntu/AmpliconRepository-prod   # or AmpliconRepository-dev
./start-server.sh

This launches a gunicorn container named amplicon-${AMPLICON_ENV} with the source checkout mounted at /srv/. Confirm it is running with docker ps. Logs are written to the logs/ directory in the checkout root.

1. How to start the server

• SSH into the EC2 instance (called ampliconrepo-ubuntu-20.04)
  • this requires a PEM key
• Go to project directory

cd /home/ubuntu/caper/

• Check to see if the Docker container is running

docker ps (look for a container called amplicon)

• If it is not running, run the start script

./start-server.sh

2. How to stop the server

• SSH into the EC2 instance (called ampliconrepo-ubuntu-20.04)
  • this requires a PEM key
• Go to project directory

cd /home/ubuntu/caper/

• Check to see if the Docker container is running

docker ps (look for a container called amplicon)

• If it is running, run the stop script

./stop-server.sh

3. How to update the server

• Clone repo using https, ssh, or GitHub Desktop to your local machine
• Make changes locally
• Push changes to the main branch of the repository
• Create a release on GitHub
  • login to github and go to the releases page at https://github.com/AmpliconSuite/AmpliconRepository/releases.
  • Create a new release using a tag with the pattern v.._ e.g. v1.0.1_072523 for version 1.0.1 created July 15, 2023.
  • This will create a tag on the contents of the repo at this moment
  • a github action will update and commit the version.txt file with the date, tag, commit ID and person doing the release and apply the tag to the updated version.txt
• After the release is published, wait for the "On Release" GitHub Action to finish before deploying. The action force-moves the release tag to the auto-generated caper/version.txt commit.
• In the site admin UI, go to /admin-prepare-shutdown/, confirm no background tasks are running, and enable shutdown mode before restarting the server. Shutdown mode prevents new project creation/editing while deployment is in progress and persists across the restart.
• SSH into the EC2 instance (called ampliconrepo-ubuntu-20.04 in us-east-1)
  • this requires a PEM key
• Go to project directory

cd /home/ubuntu/AmpliconRepository-prod/ source caper/config.sh

• Pull your changes from Github

git fetch --tags --force origin git checkout tags/<release tag in github>

• If requirements.txt or Dockerfile changed, rebuild the Docker image from the build-only checkout before restarting:

cd /home/ubuntu/ampRepo_for_docker_build/AmpliconRepository git fetch --tags --force origin git checkout tags/<release tag in github> source /home/ubuntu/AmpliconRepository-prod/caper/config.sh docker build -t genepattern/amplicon-repo:${AMPLICON_ENV} .

• For source-only changes, restart the server with the same script as the nightly cron. During server startup it automatically syncs static files to S3:

/home/ubuntu/stop-and-start-repo.sh

• If the Docker image was rebuilt, remove and recreate the app container so it uses the new image:

cd /home/ubuntu/AmpliconRepository-prod/ source caper/config.sh docker stop amplicon-${AMPLICON_ENV} docker rm amplicon-${AMPLICON_ENV} ./start-server.sh

• Verify the running container was recreated from the expected image and, when dependencies changed, verify the installed package version:

docker ps --filter name=amplicon-${AMPLICON_ENV} docker exec amplicon-${AMPLICON_ENV} bash -lc 'source /opt/venv/bin/activate && python -c "import AmpliconSuiteAggregator as a; print(a.__version__)"'

• Smoke-test the site, then return to /admin-prepare-shutdown/ and disable shutdown mode.

4. Manual disk space cleanup

The server writes temporary working directories under ./tmp/ (relative to the project root) during project creation and editing. These are cleaned up automatically by the server, but if disk space runs low you can reclaim it manually. Always check that no project creation or editing is in progress before deleting anything. First, SSH into the EC2 instance and check for active background tasks:

cd /home/ubuntu/AmpliconRepository-prod/caper
python manage.py shell -c \
  "from caper.background_tasks import get_background_task_status; import json; print(json.dumps(get_background_task_status(), indent=2))"

If active_count is 0, it is safe to remove all temp directories. To see how much space they are using and then remove them:

du -sh ./tmp/*/          # check sizes
rm -rf ./tmp/*/          # remove all temp dirs

If you want to be cautious and leave any directories that may belong to a recently-started task (for example, if you are unsure whether active_count reflects all workers), limit deletion to directories that have not been written to in at least two hours:

find ./tmp -mindepth 1 -maxdepth 1 -type d -mmin +120 -exec rm -rf {} +

Note that restarting the server (/home/ubuntu/stop-and-start-repo.sh) also triggers an automatic cleanup of any orphaned temp directories left by previous runs.