kamyh / master

Master Thesis

Master Thesis -- Dockerisation d'environement pour Les projets de bioinformatique

Architecture

Installations

Docker

Install Docker Engine

$ sudo apt-get update
$ sudo apt-get install apt-transport-https ca-certificates
$ sudo apt-key adv --keyserver hkp://p80.pool.sks-keyservers.net:80 --recv-keys 58118E89F3A912897C070ADBF76221572C52609D

$ sudo apt-add-repository 'deb https://apt.dockerproject.org/repo ubuntu-xenial main'
$ sudo apt-get update
$ sudo apt-cache policy docker-engine
$ sudo apt-get install -y docker-engine
$ sudo systemctl status docker

You now should see:

● docker.service - Docker Application Container Engine
   Loaded: loaded (/lib/systemd/system/docker.service; enabled; vendor preset: enabled)
   Active: active (running) since Wed 2016-11-30 01:28:41 CET; 8h ago
     Docs: https://docs.docker.com
 Main PID: 1171 (dockerd)
    Tasks: 41
   Memory: 3.7G
      CPU: 1min 18.316s
   CGroup: /system.slice/docker.service
           ├─ 1171 /usr/bin/dockerd -H fd://
           ├─ 1607 docker-containerd -l unix:///var/run/docker/libcontainerd/docker-containerd.sock --shim docker-con
           └─21678 docker-containerd-shim 1ed0c2cbc7dbd228de8ffd82a822df63abc6f75f3978b96a8b9e82832489a343 /var/run/d

Configure Docker for your loggedin user

$ sudo usermod -aG docker $(whoami)

You now have to reboot your machine.

Install Docker-compose (1.9)

$ curl -L "https://github.com/docker/compose/releases/download/1.9.0/docker-compose-$(uname -s)-$(uname -m)" -o /usr/local/bin/docker-compose
$ sudo chmod +x /usr/local/bin/docker-compose
$ docker-compose --version

You now should see:

docker-compose version: 1.9.0

Deploy

Get de source

$ git clone https://github.com/kamyh/master.git
$ cd master/developpement/dockers/core/data-hmm/
$ sh get_pfam_hmm.sh
$ cd ../../database/data/
$ wget https://www.dropbox.com/s/mzt9pxpfnvxl3wa/bacteriaVD.sql?dl=0
$ mv bacteriaVD.sql?dl=0 bacteriaVD.sql

Edit Configuration

You have to rename and edit the configuration file (config.example.ini)

$ cd ../../../inphinity/v_0.5
$ cp configs/config.ini.example config.ini
$ sudo nano configs/config.ini

You have to set the variable 'path_to_core' to the correct path to the core directory (/developpement/dockers/core).

Running Docker compose

Now we can start our application using docker-compose.

$ cd ../../compose/
$ sudo sh run.sh
$ docker ps

You should see this:

CONTAINER ID        IMAGE               COMMAND                  CREATED             STATUS              PORTS                              NAMES
6817333ab720        compose_core        "/bin/bash"              11 seconds ago      Up 7 seconds                                           inphinity-core
b494735f1440        compose_database    "tini -- /bin/bash /o"   12 seconds ago      Up 10 seconds       3309/tcp, 0.0.0.0:3309->3306/tcp   inphinity-database

Go to inphinity-core Docker container

$ docker exec -it inphinity-core /bin/bash

Run

$ python3 inphinity/v_0.5/app.py 

.