mampok 3.0.4

Kubernetes deployment manager for bioinformatics tools

Mampok (Managing Multiple Projects On Kubernetes) deploys containerized bioinformatics tools — Cellxgene, Jupyter, RStudio, IGV, and more — on a Kubernetes cluster backed by S3-compatible object storage. You describe your project in a JSON file (a Mamplan); Mampok handles S3 uploads, Kubernetes resource creation, pod readiness checks, and lifecycle management.

For more information about Mampok, please see the documentation.

How to install

Via Python package

Mampok is published in the Python Package Index (PyPI) under the name mampok. It can be installed with the following command:

pip install mampok

Via repository

You can install Mampok directly from the repository with the following commands:

1. Clone the repository:

git clone https://github.com/loosolab/MAMPOK

2. Move to the new repository directory:

cd MAMPOK

3. Install:

pip install .

Quick start

1. Create a config file (pass its path to every command via --config):

{
  "cluster": {
    "MY_CLUSTER": {
      "host": "ingress.example.com",
      "namespace": "mampok",
      "kubeconfig_path": "/home/user/.kube/my-cluster-config"
    }
  },
  "s3": {
    "endpoint": "https://s3.example.com",
    "access_key": "my-access-key",
    "secret_key": "my-secret-key",
    "secretname": "s3-credentials",
    "prefix": "mampok"
  },
  "mamplates_path": "/path/to/mamplates/",
  "lifetime_days": 30,
  "mampok_version": ">=2.0.0,<3.0.0"
}

2. Create a Mamplan:

mampok create-mamplan \
  --project-id my-project \
  --tool cellxgene \
  --cluster MY_CLUSTER \
  --owner jdoe \
  --datatype scRNA-seq \
  --files data.h5ad \
  --output ~/mamplans/ \
  --config /path/to/config.json

3. Deploy:

mampok deploy ~/mamplans/my-project-mamplan.json --config /path/to/config.json