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