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.
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:
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.
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.
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.
-
Install miniconda (skip if already available). Instructions here
-
Install environments
conda create -f envs/ha_py27.yml
conda create -f envs/ha_py36.yml
# Optional (removes temp files)
conda clean -a
- 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