Installing RDPTools

News Flash! – Now there is a Docker version of RDPTools that is easier to install than the native version described below. See installation instructions at https://jfq3.gitbook.io/rdptools-docker/.

RDPTools must be run in a Linux-like environment, e.g. a cluster at your own institution, Mac OS X, or Ubuntu. If you are using Windows, you may install Ubuntu inside Oracle Virtual Box or install Ubuntu as part of a dual boot system. Alternatively, with Windows 10 you may be able to install WSL2 with Ubuntu. When installing Ubuntu be sure to choose an LTS (Long Term Service) version. These are normally supported for three years, while other versions are supported for only a few months.

Processing large data sets with some RDPTools commands requires more memory than is available on notebook computers. Still, installing RDPTools on your own computer allows you to get familiar with the commands and to test scripts with smaller data sets before committing jobs to a cluster.

Required Programs

RDPTools and its dependencies are available at these URLs:

Python 2.7 is included in most Linux systems including Ubuntu 16.04 LTS, the latest LTS version as of July 2017. Test for it by typing “python” and Enter or Return in the terminal window. Exit python by entering Control D.

Install Java

You may test for the installation of Java by entering:

java

which should return a list of instructions. If it does not, install Java by entering the following in the terminal window:

sudo apt-get install default-jdk

HMMER 3.1

Install HMMER 3.1 by entering the following in the terminal:

sudo apt-get install hmmer

Check that HMMER is installed:

man -k hmmer

which should return a list of commands.

UCHIME

Create a directory for UCHIME. You will likely need to use the sudo command:

sudo mkdir /usr/local/uchime

Download the Linux binary UCHIME into the /usr/uchime directory. You can use the wget command to do this (below) or use your browser to download the file and then move it into the /usr/uchime directory. As of July 2017, the UCHIME version is UCHIME4.2.40_linuxi86.

cd /usr/local/uchime
sudo wget http://drive5.com/uchime/uchime4.2.40_i86linux32

From the uchime directory, use the sudo command to change the file permissions so that it is executable:

sudo chmod 755 uchime4.2.40_i86linux32

You may then edit the name of the file to make it shorter if you want. For example, change it to simply uchime:

sudo mv uchime4.2.40_i86linux32 uchime

Install USEARCH Version 8.1

While not part of RDPTools proper, you will need USEARCH8.1 to run the command line tutorial for the RDP pipeline. This is the last version of USEARCH to include the  -uchime_ref command for removing chimeric sequences in reference mode. To install:

cd ~/Downloads
wget https://drive5.com/downloads/usearch8.1.1861_i86linux32.gz
gzip -d usearch8.1.1861_i86linux32.gz
chmod 755 usearch8.1.1861_i86linux32
sudo mv usearch8.1.1861_i86linux32 /usr/local/bin/usearch8.1

To use USEARCH8.1’s -uchime_ref command you will also need a set of reference sequences. The tutorial for processing 16S sequences makes use of the rdp_gold.fa file placed in directory $HOME/resources. Download and place it there with the commands:

cd
mkdir resources # If you have not already created this directory
cd resources
wget https://www.drive5.com/uchime/gold.fa
mv gold.fa rdp_gold.fa

Preliminaries

Installation of RDPTools depends on the programs git and ant, so you may have to install them first. To test if git is already present, type “man -k git” followed by Enter in the terminal window. If “nothing appropriate” is returned, you will have to install git. Test for the presence of ant in the same way.

If necessary, install ant and git by entering the following in the terminal window:

sudo apt-get update
sudo apt-get install git
sudo apt-get install ant

Install RDPTools

Begin installation of RDPTools by cloning them from the Git repository. The commands below will install RDPTools in the directory usr/local:

cd /usr/local
sudo git clone https://github.com/rdpstaff/RDPTools.git

Then for a new installation of RDPTools, enter:

cd RDPTools
sudo git submodule init
sudo git submodule update
sudo make

Alternatively, to update an existing installation of RDPTools:

cd /usr/local/RDPTools
sudo git pull
sudo git submodule update
sudo make clean
sudo make

Xander is one of the RDPTools. Test for the installation of Xander by entering:

java -Xmx2g -jar /usr/local/RDPTools/hmmgs.jar

which should return a list of Xander commands.

Patched HMMER 3.0

Installation of a patched version of HMMER version 3.0 is necessary only if you intend to add capability for genes not already in the Xander installation. If you are not comfortable doing so, skip this installation and get help from the RDP staff.

To proceed on your own, download HMMER 3.0 from hmmer.org/download.html. It is in the form of a compressed file named hmmer-3.0.tar.gz.

Place the compressed file in the directory /usr/local.

sudo mv ~/Downloads/hmmer-3.0.tar.gz /usr/local/

Extract the file:

cd /usr/local
sudo tar xzf hmmer-3.0.tar.gz

This will create a directory named hmmer-3.0. Rename the directory hmmer-3.0_xanderpatch.

sudo mv hmmer-3.0 hmmer-3.0_xanderpatch

Apply the patch (the following is entered all on one line):

sudo patch /usr/local/hmmer-3.0_xanderpatch/src/p7_prior.c < /usr/local/RDPTools/Xander_assembler/bin/hmmer-3.0_Xander_patch.txt

Install the patched version following the instructions in the INSTALL file. You will likely need to use sudo. Essentially, the instructions are:

cd /usr/local/hmmer-3.0_xanderpatch
sudo ./configure
sudo make
sudo make install

The patched 3.0 version will be installed in /usr/local/bin/.
If you followed the instructions above, the original 3.1 version is in /usr/bin/.
This is important to remember when using HMMER because commands for the two versions have the same names. The directories must be specified when using either of the two versions of HMMER.