Deploy on a local server (bare metal)

This tutorial provides an overview of the steps involved in setting up a CRE on a local server (bare metal) using command-line.

Note: Please follow Starting a PhenoMeNal CRE on a public or private cloud provider for the general prerequisites for a deployment on a private of public cloud provider.

Deploy on Bare metal (KVM)

This tutorial provides an overview of the steps involved in setting up a CRE on a local server (bare metal) using command-line.

Note: Please follow Starting a PhenoMeNal CRE on a public or private cloud provider for the general prerequisites for a deployment on a private of public cloud provider.

Server specific prerequisites

• You have a Linux server (tested on Ubuntu 16.04 and Centos 7) with KVM and libvirt installed.

Configuration

All of the commands in this documentation are meant to be run in the config directory created by the command below.

Start by creating a configuration directory:

kn --preset phenomenal init kvm my-vre-config-dir
cd my-vre-config-dir

Inside this configuration directory you will need to edit the file config.tfvars where you will need to set:

Cluster

• cluster_prefix: every resource in your tenancy will be named with this prefix

Master configuration

• master_vcpu: number of virtual cpu:s to assign
• master_memory: size of memory to assign (in Megabyte, MB)
• master_as_edge: master is acting as gateway for accessing services

Storage configuration

• master_extra_disk_size: an extra virtual disk image is created and attached to VM as storage for PhenoMenal services

Cloudflare (optional) - See: KubeNow Cloudflare documentation.

• use_cloudflare: wether you want to use cloudflare as dns provider
• cloudflare_email: the mail that you used to register your Cloudflare account
• cloudflare_token: an authentication token that you can generate from the Cloudflare web interface
• cloudflare_domain: a zone that you created in your Cloudflare account. This typically matches your domain name (e.g. somedomain.com)
• cloudflare_subdomain: "a subdomain for this deployment"

Cloudflare proxy (optional) - See: KubeNow Cloudflare proxy documentation.

• cloudflare_proxied:: to proxy or not, e.g. true
• cloudflare_record_texts: name on services to be proxied

In the provision sub-section of the config.tfvars config file you can edit the following parameters: (Also see KubeNow Provisioning documentation.)

Services

• password_all_services: password for all your services (e.g. Galaxy, Jupyter etc.)
• username_all_services: username for all your services (e.g. Galaxy, Jupyter etc.)

Galaxy

• galaxy_include: should service be deployed in cluster (true/false)
• galaxy_admin_email: the local galaxy admin (you?)

Jupyter

• jupyter_include: should service be deployed in cluster (true/false)

Luigi

• luigi_include: should service be deployed in cluster (true/false)

Kubernetes dashboard

• dashboard_include: should service be deployed in cluster (true/false)

Logging and monitoring services - See: Logging and monitoring wiki

• logmon_include: should service be deployed in cluster (true/false)

Pachyderm + Minio (optional) - See: Pachyderm tutorial with MTBLS data

• pachyderm_release_name: a release name for the Pachyderm service
• pachyderm_etcd_pvc_size: storage dedicated for etcd (In GB)
• minio_release_name: release name for the Minio service
• minio_pvc_size: storage dedicated for the Minio service (In GB)
• minio_accesskey: access key for the S3 endpoint
• minio_secretkey: secret key for the S3 endpoint
• minio_replicas: number of replicas of the Minio service

Once you are done with your settings you are ready to deploy the cluster:

kn apply

when deployment is finished then you should be able to reach the services at:

Galaxy         = http://galaxy.<your-prefix>.<yourdomain>
Jupyter        = http://notebook.<your-prefix>.<yourdomain>
Luigi          = http://luigi.<your-prefix>.<yourdomain>
Kube-dashboard = http://dashboard.<your-prefix>.<yourdomain>
Pachyderm      = ssh into the master node and use pachctl. Pachyderm tutorial: https://github.com/phnmnl/MTBLS233-Pachyderm

and if you want to ssh into the master node:

kn ssh

and to destroy use:

kn destroy

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