Installation.md

Nextflow needs to be installed to run this pipeline. Nextflow can be used on any POSIX compatible system (Linux, OS X, etc). It requires BASH and Java 8 (or higher) to be installed.

Nexflow Installation:

Execute the following steps to install nextflow on your machine

# Check java version (needs 1.8 or higher)
java -version

# Download and install nextflow
wget -qO- get.nextflow.io | bash

# (Optional) move the file to a $PATH accessible directory
sudo mv nextflow /usr/local/bin/

There are several ways to install the Tools needed by the pipeline:

Docker installation:

Using the docker container system is the most convenient way to run this pipeline. Install docker using the package manager of your system or look on their (homepage)[https://docs.docker.com/install/] for more specific installation procedures.

Singularity installation:

If runnign docker on your machine is not possible or desirable (i.e. on high performance cluster machines) you can use [Singularity](https://singularity.lbl.gov/install-request nstead). See the homepage for installation procedures.

Local installation using conda:

These steps are only necessary when you dont want to use docker/singularity. All the tools needed are contained in two conda environments located in the env/ Folder. Install them so you can call them from you path later.

1. Install miniconda (skip if already available). Instructions here

2. Install environments

conda create -f envs/ha_py27.yml
conda create -f envs/ha_py36.yml

# Optional (removes temp files)
conda clean -a

3. Download required database

Download and include CARD-Antibiotic resistance database for rgi

wget -q -O card-data.tar.bz2 https://card.mcmaster.ca/latest/data
tar xfvj card-data.tar.bz2

source activate ha_py27 
rgi load --afile card.json 
source deactivate ha_py27