Installation

Centrifuger is distributed both as a Bioconda package and as source code that compiles with a single make. Either route gives you the same four executables: centrifuger-build, centrifuger, centrifuger-quant and centrifuger-download.

Requirements#

• A Linux or macOS system with a C++ compiler and make.
• pthreads — Centrifuger's only dependency, and present by default on essentially every Unix-like system.
• Enough RAM to hold the index you intend to use. This is the real constraint: see how much memory do I need?

Install with Conda (recommended)#

Centrifuger is available from Bioconda:

conda install -c conda-forge -c bioconda centrifuger

Installing into a dedicated environment keeps it isolated from the rest of your tooling:

conda create -n centrifuger -c conda-forge -c bioconda centrifuger
conda activate centrifuger

Mamba works as a drop-in replacement and resolves the environment considerably faster:

mamba install -c conda-forge -c bioconda centrifuger

Build from source#

Clone the GitHub repository and run make in it:

git clone https://github.com/mourisl/centrifuger.git
cd centrifuger
make

The executables are written into the directory you just built in. There is no make install step.

Putting Centrifuger on your PATH#

After building, you can run the programs by their full path — /path/to/centrifuger/centrifuger — but it is more convenient to make them available everywhere. Either add the build directory to PATH:

export PATH="/path/to/centrifuger:$PATH"

(add that line to your ~/.bashrc or ~/.zshrc to make it permanent), or create a symbolic link from a directory that is already on PATH:

ln -s /path/to/centrifuger/centrifuger ~/bin/centrifuger

Verify the installation#

Run a program without arguments to print its usage message:

centrifuger
centrifuger-build
centrifuger-quant

For an end-to-end check, use the example/ directory included in the source distribution — it contains a tiny reference, a taxonomy and a pair of FASTQ files, and the whole test takes seconds. The quick start walks through it.

Keeping up to date#

Conda installations update in the usual way:

conda update -c conda-forge -c bioconda centrifuger

Source installations update by pulling and rebuilding:

cd /path/to/centrifuger
git pull
make clean && make

Next steps#

• Quick start — your first classification.
• Pre-built indexes — download a database instead of building one.