Local Docker deployment package for OrthoVenn4.

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This guide covers the normal installation path for OrthoVenn4 from the deployment package. It focuses on preparing the deployment directory, starting the platform, creating the administrator account, and checking that the workflow service is ready.

Before installation, prepare:

• Docker and Docker Compose
• A Linux, macOS, or server host with enough CPU, memory, and disk space

Recommended minimum for a small test deployment:

For a new server, use the installer script. It downloads the deployment package to ~/orthovennplus by default, prepares .env, installs the reference database, and starts the Docker services.

Global source:

curl -fsSL https://raw.githubusercontent.com/Yonkers/orthovennplus/main/tools/install_bootstrap.sh | bash -s -- --region global

Mainland China source:

curl -fsSL https://gitee.com/leeoluo/orthovennplus-docker/raw/main/tools/install_bootstrap.sh | bash -s -- --region cn

If --region is omitted, the installer tests GitHub and Gitee connectivity and chooses a default region automatically.

After installation, open:

http://<server-ip>:5920

Use the manual steps below when you need to inspect or customize the deployment package before starting services.

Clone or unpack the deployment package on the server. Choose one source:

# GitHub
git clone https://github.com/Yonkers/orthovennplus.git orthovennplus-docker
cd orthovennplus-docker

# Gitee mirror, recommended for mainland China
git clone https://gitee.com/leeoluo/orthovennplus-docker.git orthovennplus-docker
cd orthovennplus-docker

The deployment directory should use this layout:

orthovennplus-docker/
|-- run.sh
|-- docker-compose.yaml
|-- .env
|-- .env.example
|-- install_refdb.sh
|-- install_sonic_pfam_profiles.sh
|-- setup_uniprot_refdb.py
|-- docker/
|   |-- nginx/
|   |   |-- default.conf
|   |   |-- frontend.conf.template
|-- tools/
|   |-- install.sh
|   |-- install_bootstrap.sh
|-- data/                     # created during installation/runtime
|   |-- refdb/                # reference data installed by install_refdb.sh
|   |-- projects/
|   |-- uploads/
|   |-- logs/
|-- README.md

The files under data/refdb are used by GO annotation and DIAMOND-based annotation. They are distributed as release assets instead of Git-tracked files, so the repository stays small while installation remains reproducible.

If the scripts are not executable after cloning or unpacking a release package, set the executable bit before running any installer or startup script:

chmod +x run.sh install_refdb.sh install_sonic_pfam_profiles.sh tools/install*.sh

The deployment package includes a ready-to-use .env file. For a standard single-server deployment, you can keep the defaults and continue.

Optional: edit .env if you need to change the web port, storage policy, upload domain, email service, or other deployment details. See Advanced Configuration.

If .env is missing, create it from the example file: cp .env.example .env

Install the required reference data. The installer chooses the default download source by region: global installations use GitHub first, mainland China installations use Gitee first, and both fall back to the official OrthoVenn4 web source if needed:

./install_refdb.sh

To force GitHub release downloads:

./install_refdb.sh --source github

For servers in mainland China, you can use the Gitee release source:

./install_refdb.sh --source gitee

If the release asset is unavailable and you need to generate the UniProt reference files manually, run:

python setup_uniprot_refdb.py

SonicParanoid2 works in graph-only mode by default. If you plan to use full SonicParanoid2 architecture/domain mode, install the optional Pfam profile database later from Optional SonicParanoid2 Pfam Profile DB.

The recommended startup command is run.sh. On most servers, run it with sudo. The script creates required data directories, pulls images, runs database migrations, normalizes writable data directory permissions, and starts the Docker Compose services:

Start the services:

sudo ./run.sh

By default, run.sh pulls images from Docker Hub. If the server is in mainland China or Docker Hub access is slow, use the Aliyun mirror registry:

sudo ./run.sh --registry aliyun

Check the available options:

./run.sh --help

After the services start, open:

http://<server-ip>:5920

Check service status when needed:

sudo docker compose ps

Use this only when you do not want to use run.sh:

mkdir -p data/projects data/uploads data/uploads/tus data/tmp data/logs data/refdb data/builtin_db data/postgres
mkdir -p data/refdb/sonicparanoid2
docker compose up -d postgres redis
docker compose run --rm backend alembic upgrade head
docker compose up -d

Most deployments can keep the default .env file. Edit it only when you need to adapt ports, credentials, upload behavior, resource usage, cleanup policy, or email service.

Common settings:

If you change .env after services are already running, restart the stack:

sudo ./run.sh --skip-pull --skip-migrate

You need one administrator account to manage users, settings, workers, project cleanup, and gallery projects.

By default, the first registered user becomes the administrator:

FIRST_REGISTERED_USER_AS_ADMIN=true

You can also create an administrator with the backend CLI:

docker compose exec backend \
  env ORTHOVENN_ADMIN_PASSWORD='your-strong-password' \
  python -m app.cli create-admin \
  --username admin \
  --email admin@example.com

To promote an existing user:

docker compose exec backend \
  env ORTHOVENN_ADMIN_PASSWORD='your-strong-password' \
  python -m app.cli create-admin \
  --username existing-user \
  --email existing@example.com \
  --promote-existing

SonicParanoid2 uses graph-only mode by default and does not need the Pfam profile database. Install the Pfam MMseqs profile database only if you plan to disable graph-only mode and run the full architecture/domain workflow.

Check the current status from the deployment directory:

./install_sonic_pfam_profiles.sh status

The script only uses these paths:

data/refdb/sonicparanoid2/downloads/
data/refdb/sonicparanoid2/pfam_profile_db/

The recommended path is manual download first, then local install.

Manual download address:

https://drive.google.com/file/d/1eV3t2FINOUPJI1132w3bmBrHnO3_bpfJ/view?usp=sharing

Save the archive as:

data/refdb/sonicparanoid2/downloads/sonicparanoid2_pfam_mmseqs_profile_db.tar.gz

Then verify and install:

mkdir -p data/refdb/sonicparanoid2/downloads
tar -tzf data/refdb/sonicparanoid2/downloads/sonicparanoid2_pfam_mmseqs_profile_db.tar.gz >/dev/null
./install_sonic_pfam_profiles.sh install

If the archive was downloaded to another location:

./install_sonic_pfam_profiles.sh install /path/to/sonicparanoid2_pfam_mmseqs_profile_db.tar.gz

If the server can access Google Drive directly, you can try downloading with curl:

mkdir -p data/refdb/sonicparanoid2/downloads
curl -L \
  'https://drive.google.com/uc?id=1eV3t2FINOUPJI1132w3bmBrHnO3_bpfJ' \
  -o data/refdb/sonicparanoid2/downloads/sonicparanoid2_pfam_mmseqs_profile_db.tar.gz
./install_sonic_pfam_profiles.sh install

If graph-only mode is disabled but the profile database is missing, the SonicParanoid2 task will stop early and report the missing profile database path.