1.2 Installation from source

1.2.1 Requirements

ATLAS requires the following programs/libraries to be pre-installed. If you do not have root access, you can install them locally.

  • A compiler which is compatible with C++17 or higher.
    We recommend gcc (version 9 or higher) or clang (version 5 or higher). You can check the pre-existing version on your system with gcc --version or clang --version.

  • cmake, version 3.14 or higher.
    You can check the pre-existing version on your system with cmake --version.

1.2.2 Platforms

  • On Linux computers, you should be able to install atlas witout any difficulties.

  • On Windows computers, use the Windows Subsystem for Linux.

  • On Mac computers, use Homebrew to install samtools, cmake, autoconf and automake:

brew install samtools cmake autoconf automake

  • On most computing clusters, you can load recent cmake and gcc versions using modules.

  • You can also install the required build-tools and libraries using conda, however, it’s probably easier to just install atlas directly using conda (see above)

1.2.3 Download

ATLAS is hosted on bitbucket and can be downloaded with the command:

git clone --depth 1 https://bitbucket.org/WegmannLab/atlas.git

1.2.4 Compile

After cloning, navigate into the atlas folder (cd atlas) and execute the following commands:

mkdir -p build
cd build
cmake ..
make

If your platform has multiple cores, you can speed up the compilation using make -j<N>, where N is the number of physical cores.

If the ninja build-system is installed on your platform, you can alternatively build using ninja instead of make, which will speed up the compilation:

mkdir -p build
cd build
cmake .. -GNinja
ninja

1.2.5 Compile using conda

As an alternative to using a locally installed compiler, you can also compile atlas using a conda environment:

conda env create -f conda.yml
conda activate atlas 
mkdir -p build
cd build

As cmake and conda do not play together nicely, you need to tell cmake where conda puts its binnaries and libraries:

cmake .. -GNinja -DCONDA=ON -DCMAKE_C_COMPILER=$(which gcc) -DCMAKE_CXX_COMPILER=$(which g++) -DCMAKE_LIBRARY_PATH=$CONDA_PREFIX/lib -DCMAKE_INCLUDE_PATH=$CONDA_PREFIX/include
ninja

1.2.6 Update

ATLAS is under active construction. Obtain the newest version by pulling and compiling again:

cd atlas/build
git pull
make