Installation
The easiest way to install MinVar is via bioconda. Click on the image above and follow the instructions there.
Here below we explain how to install with ansible.
A condensed list of dependencies
- python 3.x
- pandas
- BLAST
- samtools
- GATK
- picard-tools
- bwa
- lofreq
Setting up with Ansible
The directory ansible
in the project repo provides an easy option to set up MinVar with
its dependencies on a dedicated machine. The files therein define an
ansible play for this purpose.
What is Ansible
Ansible is a deployment tool that allows an automatic provisioning of machines on the cloud (it can be used on AWS, DigitalOcean, Google Cloud Platform etc.). The user installs it on a local machine (this can be your old laptop), defines commands in specific files and uses them to set up a remote machine.
In the following we will assume that you have installed ansible on your local laptop and you want to set up MinVar on a remote machine running Linux Ubuntu 16.04. The access to this machine is provided by private-public SSH key pair that must be set up. Good instructions for this task can be found in this help.
How to proceed
- Install ansible on your machine (on Mac OS X you can do it via the package
manager brew with
brew install ansible
), - clone MinVar from GitHub with
git clone https://github.com/ozagordi/MinVar.git
or download/unzip it, - move to the directory
ansible
in the cloned repository and identify the filehosts
. This file contains two lines[minvarmachine]
and a fake ip address. Edit the address to the one of the machine you want to setup, - in the same directory edit the file
setup-hosts.sh
: adapt--key-file=path_to_your_private_key
to point to your personal private key, - copy your personal public key into
my.key.pub
, - run
./setup-hosts.sh
.
What can go wrong
We assumed that you have an Ubuntu 16.04 available. Most of the stuff will work on Ubuntu 14.04, but you might run into troubles because of different versions of Java (you can find a good tutorial on this here).
UNREACHABLE!
usually means that the private/public key pair does not work.
You must be able to ssh into the remote machine with this command (edit accordingly)
ssh -i path_to_your_private_key ubuntu@remote_ip_address
If you don't want to use ansible
The ansible playbook reads almost as plain English. You can manually copy the instructions from there and install what you need.