Installation & requirements

DIAMOND compiles as generic C++ code and has no particular requirements on the hardware architecture, but it makes use of the SSE instruction set of the Intel/AMD x86-64 platform if available and will run considerably faster on that platform. It runs on POSIX-compatible operating systems (Linux, FreeBSD, OS X) as well as on Microsoft Windows.

A high-memory server is recommended for better performance, but the program can be run on standard desktop computers or laptops.

Compiled binaries are available for download for Linux, macOS (via Bioconda), FreeBSD (via pkg) and Windows. For best performance, it is recommended to compile the software from source on the target system.

The software has been tested on Ubuntu 18.04 bionic, Ubuntu 14.04 trusty, CentOS 7, macOS 10.13 and Microsoft Windows 10.

Binary download

Linux

A precompiled binary is available for recent Linux systems and may be downloaded for immediate use:

wget http://github.com/bbuchfink/diamond/releases/download/v2.0.4/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz

If the binary does not work on your system, i.e. you are getting error messages like Kernel too old, please try another installation method or compile the software from source.

Linux/macOS (via Bioconda)

Install Bioconda on your system if not already present, then install DIAMOND using this shell command:

conda install -c bioconda diamond

Regularly updating to the latest version is also recommended:

conda update diamond

Linux (via Docker)

To pull the latest version of the official Docker container:

docker pull buchfink/diamond

To pull a specific version:

docker pull buchfink/diamond:version2.0.4

FreeBSD

On FreeBSD, you can use pkg install diamond to install the software.

Windows

A binary executable for Windows can be downloaded at the GitHub Releases page. You also need to install the Visual C++ Redistributable.

Compiling from source

Compilation requires GCC 4.8.1 or later, CMake 2.6 or later as well as libpthread and zlib including development headers. To compile DIAMOND from source, invoke the following commands on the shell:

wget http://github.com/bbuchfink/diamond/archive/v2.0.4.tar.gz
tar xzf v2.0.4.tar.gz
cd diamond-2.0.4
mkdir bin
cd bin
cmake ..
make -j4
sudo make install

Note:

• The typical time for compilation is 3-4 minutes using one core.
• Use cmake -DCMAKE_INSTALL_PREFIX=... to install to a different prefix.
• Use cmake -DCMAKE_BUILD_MARCH=native to perform a native compile.
• By default, a portable binary will be created that contains separate code paths for systems that support SSE4.1, AVX2, or neither. Be aware that more recent versions of GCC may use AVX2 instructions even for generic builds. In these cases, you need to use -DCMAKE_BUILD_MARCH=nocona for a binary compatible with host CPUs supporting only SSE3, and -DCMAKE_BUILD_MARCH=nehalem for compatibility with host CPUs supporting SSE4.2.