Pre requisite installations - picrust/picrust2 GitHub Wiki

Note: this page has been left for legacy purposes but is no longer required.

This page lists instructions on how to install the pre-requisites for PICRUSt2. The three tools described below are used for the place_seqs.py pipeline and the source code is already in the PICRUSt2 repo in placement_tools.

All of these tools need to be installed before PICRUSt2 installation

Commands below are assuming that you are working in a Linux environment. These commands should work for most users, but if you run into errors you should check the relevant tool's website.

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:

cd placement_tools

EPA-NG installation

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/

*Note: if the make command fails then you likely need to install various packages for compilation: sudo apt-get install autotools-dev libtool flex bison cmake automake autoconf

GAPPA installation

tar -xzf gappa-0.0.0-dev.tar.gz
cd gappa-0.0.0-dev
make
ln -s $PWD/bin/gappa ~/bin/

conda installation

The most up-to-date instructions are here: https://conda.io/docs/user-guide/install/linux.html

However for the impatient you can do the following:

wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh
(follow on-screen instructions when prompted,"enter", "yes", "yes")

All done! You can continue with the rest of the PICRUSt2 installation

OPTIONAL PaPaRa installation

If you don't have BOOST installed you'll need to install that first:

sudo apt-get install libboost-all-dev

And then install PaPaRa:

tar -xzf papara_nt-2.5-dev.tar.gz
cd papara_nt-2.5-dev
sh build_papara2.sh
ln -s $PWD/papara ~/bin/