dbOTUc

Efficient and parallelised implementation of dbOTU3.

Table of contents

• Table of contents
• Requirements
• Installation
• Usage
• License

Requirements

There are no requirements for using the pre-compiled static binaries on 64-bit linux distributions. Otherwise, there are several libraries which are required for building and running. For further information, see Compiling from source.

Installing

dbOTUc can be installed via pre-compiled binaries or from source.

GNU/Linux

For most 64-bit linux distributions (e.g. Ubuntu, Debian, RedHat, etc) the easiest way to obtain dbOTUc is via statically compiled binaries on the releases page. These binaries can be downloaded and run immediately without any setup as they have no dependencies.

Compiling from source

Compiling from source requires these libraries and software:

C++11 (gcc-4.9.0+, clang-4.9.0+, etc)
OpenMP 4.0+
GNU Scientific Library 2.1+
GNU getopt
GNU make
GNU autoconf

After meeting the above requirements, cmompiling and installing dbOTUc from source can be done by:

git clone https://github.com/scwatts/otudistclust.git
cd otudistclust
./autogen.sh
./configure --prefix=/usr/
make
make install

Once completed, the dbOTUc executables can be run from the command line.

Usage

Simple command invocation:

dbotuc -c otu_table.tsv -f otu_representative.fasta -o otu_table_clustered.tsv -m cluster_members.tsv -t 4

License

GNU General Public License v3.0