· 2019-07-28 · software distributed in docker container unit testing with continuous...

Bryan Brancotte, Thomas Menard and Hervé MénagerPoster #212

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2 | Brancotte Bryan | DevOps bioinformatics services

Why DevOps for bioinformatics services ?

Software reliability is critical for adoption.

● Tested, with unit tests● Documented (user and dev)● Reproductible● Highly available

DevOps practices help tackle these issues.

Code versioning with gitSoftware distributed in Docker containerUnit testing with Continuous integration with GitLab(Automated) Continuous deployment with Kubernetes


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Docker

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GitLab

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Kubernetes

Developer’s perspective


gitpush

CI/CD : Developer’s perspective Test (CI)

(1)*

Build(2)*

* Only when previous step ok

use

use

App

user

dev

Takeway: Press enter once, 2 minutes later your user has the new version ready to use !

Deploy

(3)*


Namespace: MyApp

Deployment

Deployment

Serviceport 8080, frontend

The world

Ingresshttps://abc.pasteur.cloud

FrontendBackend

Serviceport 5432backendPersistent

VolumeClaim

Scalable

web-app #1(replicat)



Postgres

Kubernetes concepts

● Containersrun in pods

● DeploymentHow to run containers

● ServiceHow to reach Deployments

● IngressExpose Service

● Persistent VolumeStore data


with YAML files

* or should be considered as is15 | Brancotte Bryan | DevOps bioinformatics services

YAML for the DB apiVersion: extensions/v1beta1kind: Deploymentmetadata: name: postgresspec: template: metadata: labels: app: postgres-app role: backend spec: containers: - image: "postgres:10.1" name: postgres envFrom: - configMapRef: name: postgres-config-map ports: - containerPort: 5432 name: postgres volumeMounts: - name: postgres-data-pv mountPath: /var/lib/postgresql/data volumes: - name: postgres-data-pv persistentVolumeClaim: claimName: postgres-data-pv-claim

● Deployment known as

● Use pgsql container

(already exist, maintained

by the community)

● User, pwd, stored in a

ConfigMap

● Mount a volume

● Volume is a Persistent

Volume Claim


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● Up since November 2018

● Open to the whole Institut Pasteur since January 2019

● 4 projects at the HUB○ Bacteriophage infection, CRISPR screen browser,

human protein database, Time tracking

● 10 servers, 320 cores, 2,5 TB of RAM

● 1 « GPU » Nvidia DGX1, 40 cores, 512 GB of RAM


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Why going DevOps?


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Poster 212

● https://bit.ly/2K3Clhu

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Questions ?20 | Brancotte Bryan | DevOps bioinformatics services

https://bit.ly/2K3Clhu

· 2019-07-28 · software distributed in docker container unit testing with continuous...

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