armadillo2

This is the java version of Armadillo workflow (adn.bioinfo.uqam.ca/armadillo)

armadillo2.0 and Docker

armadillo2.0 proposed NGS programs that are running in Docker containers.
Docker needs to be installed and Docker Daemon need to run. Windows only, Docker information can to be setted and tested in Armadillo Preferences or with the Docker button (top right of workflow framework)
It has been tested on:

• ubuntu 14.04, 16.04 with Docker running in user session. (More instruction on https://askubuntu.com/a/477554)
• windows7 and lower with Docker Toolbox (More instruction on https://docs.docker.com/toolbox/toolbox_install_windows/)
• mac osX sierra version 10.12.6 and Docker Community Edition 17.09.0-ce-mac35 (More instruction on https://docs.docker.com/docker-for-mac/)

armadillo2.0 and Cluster

armadillo2.0 proposed also a cluster workflow.
It's using SSH key connexion to Calcul Québec Cluster. Cluster information can to be setted and tested in Armadillo Preferences or with the Cluster button (top right of workflow framework)

test a workflow

A simple workflow is available at https://github.com/JeGoi/Armadillo_SNPs_WF_test
It can be run on local machine with Docker or on Mammouth Parallèle II (https://wiki.ccs.usherbrooke.ca/Mammouth:Accueil)

from armadillo1.1 to armadillo2.0

On mac or windows, you can use http://www.bioinfo.uqam.ca/armadillo/download.html
Then replace ./src/ ./data/ ./lib/ directories by the directories from this depot
Remove also ./config.dat and ./armadillo.log
Remove ./Armadillo.jar. Rename ./Armadillo.jar_all in Armadillo.jar
Then run Armadillo as before. On linux, just follow instruction from here: https://github.com/JeGoi/Armadillo_SNPs_WF_test/blob/master/README.md or clone (download this depot) and use Armadillo.jar_all as Armadillo.jar

NGS not on Docker

The following programs are not on Docker, you will have to add their binary files in ./executable

• Bowtie
• Bowtie2
• Cutadapt
• FastqC ... We expect to moved them on Docker quickly