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Readme_deployment.md

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IN-SYLVA infrastructure installation (debian server)

Here are instructions to deploy IN-SYLVA infrastructure on a debian server.

In the rest of this document, the server name will be "localhost". You should change it according to your needs.

Fully tested on Debian Jessie distribution

Step 1: installing docker-engine

Follow instructions given on this docker page. Nothing to change !! Recommanded version:

Docker version 19.03.5, build 633a0ea838

Make it run each time the system restart

systemctl enable docker

Step 2: installing docker-compose

Follow instructions given on this docker page.

Sometimes, this process may fail (the file is big). Retry again later !

Step 3: about security

Following explanation findable here, you should create a "docker group" and a your account in this group. Then your account will be allowed to run docker commands. Find complete security concern in docker documentation given.

export A_USER=a_user_login_able_to_run_docker_commands
groupadd docker
usermod -aG docker $A_USER
newgrp docker

Step 4: Getting tools from gitlab

All code are stored on the forgeMIA gitlab repository. It is accessible through this URL: https://forgemia.inra.fr The IN-SYLVA project is stored as a "private project". Therefore one need an account to gain access. Please follow instructions given on the main page, using the "sign in" (connexion SSO) process [uses your ldap authentication data]. Create a dedicated directory with enough space on your server. For the rest of this document, we will guess that the IN-SYLVA infrastructure will be stored in a directory named "$insylva_dir".

Gain access to the forge, by creating a SSH public key on the server you will use to run in-sylva. The first step is to create an account to the forgemia, then ask in-sylva project manager to allow you (it's a private project). All instructions to create your key pair is given in the "user settings"/SSH keys part of the forgemia web interface.

export insylva_dir=/usr/local/insylva
cd $insylva_dir
git clone [email protected]:in-sylva-development/in-sylva.infrastructure.git

After this, all necessary packages will be available on your server

Building in-sylva.keycloak:latest

Building Keycloack docker image. This tool is needed to manage authentication for all IN-SYLVA tools.

cd in-sylva.infrastructure/keycloak && sh ./build.sh

Building in-sylva-postgres:latest

Building PostgreSQL docker image. The SGBD will be used to store various data for IN-SYLVA SI.

cd ..  && cd postgresql && sh ./build.sh

Step 5: Starting IN-SYLVA SI

cd .. && docker-compose --compatibility up -d

Step 6: Testing IN-SYLVA SI

Try to reach keycloack at http://localhost:7000/auth/ Try to reach pgadmin4 at http://localhost:5050/auth/

Managing errors

What to do if things go wrong ?

  1. Call the police
  2. Call Ozkan

Customizing / questions

Docker-compose questions
  • mongo database name: inra_paca: should be change to insylvadb or insylva_mongodb
  • mongo user name: inra_paca_mongoc: should be change to insylva or insylva_mongo_user
  • pgadmin_default_email: user should be incited to change to something else. What about the password associated with it ?
  • which instructions if we have already a postgresql server running somewhere and want to use it ? unplug the postgre container, and probably pgadmin4 also (as we may have another instance elsewhere). Need to create empty databse using the file data.sql for the structure ? Declare an account allowed to create a new database in the pgsql instance ...