PICRUSt22

PICRUSt2 wraps a number of tools to generate functional predictions from amplicon sequences. 

https://github.com/picrust/picrust2/wiki

Installation guide

https://github.com/picrust/picrust2/wiki/Installation

ssh -Y lxlogin6.lrz.de (-l userID)
module load gcc/4.9
module load python

Pre requisite installations

https://github.com/picrust/picrust2/wiki/Pre-requisite-installations

  • EPA-NG
  • GAPP

Setting up your PATH

It is presumed that you have a "bin" directory within your home directory (e.g. "~/bin") and this directory is within your PATH environment variable.

You will need to enter the directory containing these tools:

mkdir ~/DIR/placement_tools
cd placement_tools

EPA-NG installation

wget https://github.com/gavinmdouglas/epa-ng/archive/0.2.1-beta-dev.tar.gz
tar -xzf epa-ng-0.2.1-beta-dev.tar.gz
cd epa-ng-0.2.1-beta-dev
make
ln -s $PWD/bin/epa-ng ~/bin/

GAPPA installation

wget https://github.com/gavinmdouglas/gappa/archive/v0.0.0-dev.tar.gz
tar -xzf gappa-0.0.0-dev.tar.gz 
cd gappa-0.0.0-dev 
make 
ln -s $PWD/bin/gappa ~/bin/

After installing these pre-requisites, clone the repository

git clone https://github.com/picrust/picrust2.git
cd picrust2/

Install PICRUSt2 and other dependencies in a new conda environment

conda env create -f picrust2-env.yaml
source activate picrust2
pip install --editable .

Run the tests to verify installation

pytest