Install dependencies

If you are running this tutorial using Amazon EC2 instance loaded with the recommended AMI, you can skip this part.

This pipeline requires:

  • HMMER3.1
  • mothur
  • RDP mcclust
  • python pandas, numpy, scipy, matplotlib, and screed package.

Following steps should work for linux machines. If you are running this tutorial using Amazon EC2 instance loaded with the recommended AMI, you can skip this part.

This tutorial is made on a 64 bit linux (ubuntu) machine. If you have 32 bit machine, the installer file links needs to be changed for HMMER3.1 and mothur.

HMMER3.0 or lower does not work due to change in HMM format (.hmm).

Mothur 1.34.2 is used here

Setup installation directory

Clone the SSUsearch repository (Skip if you have already done so):

cd ~/Desktop
git clone https://github.com/jiarong/SSUsearch

Go to the working directory:

cd ~/Desktop/SSUsearch/

Make a directory called external_tools and go into it:

mkdir -p ./external_tools
cd ./external_tools

Install HMMER

wget -c http://selab.janelia.org/software/hmmer3/3.1b1/hmmer-3.1b1-linux-intel-x86_64.tar.gz -O hmmer-3.1b1-linux-intel-x86_64.tar.gz

tar -xzvf hmmer-3.1b1-linux-intel-x86_64.tar.gz

Copy the binary to a global PATH, you will need administrater privilege and password:

sudo cp hmmer-3.1b1-linux-intel-x86_64/binaries/hmmsearch /usr/local/bin

Install mothur

wget http://www.mothur.org/w/images/8/88/Mothur.cen_64.zip -O mothur.zip

unzip mothur.zip

Copy the binary to a global PATH, you will need administrater privilege and password:

sudo cp mothur/mothur /usr/local/bin

Install RDP mcclust tool

wget https://s3.amazonaws.com/ssusearchdb/Clustering.tgz

tar -xzvf Clustering.tgz

Install python packages

Skip if you already have the packages installed

source ~/.bashrc

pip install -U pip

pip install screed

pip install brewer2mpl

pip install biom-format

Install numpy, matplotlib, scipy, and pandas

pip install numpy matplotlib scipy pandas

Alternatively, you can install anaconda that have most popular python packages installed: https://store.continuum.io/cshop/anaconda/

The anaconda installation guide is here.

check dependencies installed

make -f SSUsearch/Makefile tool_check Hmmsearch=hmmsearch Mothur=mothur Mcclust_jar=./Clustering/dist/Clustering.jar