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Installation Instructions

Before getting started with Dahak, you will need the following software installed:

REQUIRED:

  • Docker or Singularity
  • Python 3
  • Conda
  • Snakemake

The instructions below will help you get started running the software above.



Installing Docker or Singularity

(Recommended) Singularity

Singularity is a tool for running Docker containers in higher security environments (e.g., high performance computing clusters) where permissions are restricted. If you wish to use Docker directly and have root access (e.g., with AWS/cloud machines), see the "Getting Started with Docker" section below.

Installing a stable version of Singularity is recommended. Stable versions can be obtained from Singularity's Releases on Github.

(In an HPC environment, these commands are run by the system administrator.)

# Latest
VERSION=2.5.1

# More widely available
VERSION=2.4.6

wget https://github.com/singularityware/singularity/releases/download/$VERSION/singularity-$VERSION.tar.gz
tar xvf singularity-$VERSION.tar.gz
cd singularity-$VERSION
./configure --prefix=/usr/local
make
sudo make install

To check whether Singularity is installed (in an HPC environment, this command is run by the user), check the version:

singularity --version

(Optional) Docker

If you wish to follow along with the walkthroughs, which cover the use of Docker containers to run the workflows interactively, you will need to install Docker, which requires root access.

Alternatively, Dahak provides Snakefiles for automating these workflows without requiring root access by using Singularity (see instructions above).

First, update your machine:

# Update aptitude and install dependencies
sudo apt-get -y update && sudo apt-get install zlib1g-dev ncurses-dev

Next, install Docker:

# Install Docker
wget -qO- https://get.docker.com/ | sudo sh
sudo usermod -aG docker ubuntu


Installing Python

To run Dahak workflows, we utilize Snakemake, a Python build tool. To use Snakemake, we must first install Python.

To ensure a universal installation process, we will use pyenv to install the correct versions of Python and Conda.

There are many versions of Python, so your setup may vary. We provide installation instructions using two methods:

  • Aptitude-installed Python (requires root)
  • Pyenv-managed Python (non-root)

Pyenv is a command-line tool for managing multiple Python versions, including Conda.

(Recommended) Installing Aptitude Python

To install Python with Aptitude:

sudo apt-get -y update
sudo apt-get -y install python-pip python-dev

(Optional) Installing Pyenv

Start by running the pyenv installer:

# Install pyenv 
curl -L https://raw.githubusercontent.com/pyenv/pyenv-installer/master/bin/pyenv-installer | bash

Add pyenv's bin directory to $PATH (should already be in ~/.bash_profile but just in case):

echo 'export PATH="~/.pyenv/bin:$PATH"' >> ~/.bash_profile
source ~/.bash_profile

You should see a path with a .pyenv directory in it when you type which pyenv.

You can now install various Python versions (we will install a version of Conda below):

PYVERSION="3.6.5"
PYVERSION="anaconda3-5.1.0"
PYVERSION="miniconda3-4.3.30"

To install it:

pyenv install $PYVERSION

To make it available on the $PATH (to make it the version of Python that python on the command line points to):

pyenv global $PYVERSION
eval "$(pyenv init -)"

To make this change permanent, you can add the pyenv init statement to your ~/.bash_profile:

echo 'eval "$(pyenv init -)"' >> ~/.bash_profile
source ~/.bash_profile

You should also have a version of pip associated with python:

pip install --upgrade pip


Installing Conda

Installing Conda with Python

Once Python is installed, install the latest Miniconda from continuum.io:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh

Now check to ensure conda is installed and is the correct version:

which conda
conda --version
python --version

Add the required conda channels:

conda update
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Installing Conda with Pyenv

Once pyenv is installed, use it to install Miniconda 4.3.30 with Python 3:

CONDA="miniconda3-4.3.30"
pyenv install $CONDA
pyenv global $CONDA
eval "$(pyenv init -)"

You can also add this to your bash profile to ensure that the global pyenv Python version is always the first version of Python on your path:

echo 'eval "$(pyenv init -)"' >> ~/.bash_profile
source ~/.bash_profile

Now check to make sure you have the pyenv-installed version of conda:

which conda
conda --version
python --version

Add the required conda channels:

conda update
conda config --add channels r
conda config --add channels defaults
conda config --add channels conda-forge
conda config --add channels bioconda

Create a Conda Environment

Once conda is installed, you can create a conda environment called dahak as detailed in the conda documentation:

conda create --name dahak


Installing Snakemake

Now install snakemake from the bioconda channel, or install it using pip:

conda install -c bioconda snakemake

or

pip install snakemake

Note that this pip will correspond to the version of Python and Conda that are on the path.