Usage via Repository

Usage (via repository)

We do not recommend building the tools in this project yourself as our docker container is easier and does not require the user to install any additional dependencies. The following documentation is primarily meant for users who want to extend or modify our code and thus are required to build from scratch. If you are just a normal user and the docker container does not work on your platform please do not hesitate to create a github issue so that we can extend compatibilty.

Dependencies

Before using NeEDL, you have to install the following external dependencies:

• CMake version 2.7 or higher (for compilation). Installation instructions can be found here.
• Doxygen (for creating the documentation). Installation instructions can be found here.
• OpenMP compatible C++ compiler. Under Linux, OpenMP is supported by default. Under macOS, please install libomp using Homebrew. After having installed Homebrew, open a shell and execute brew install libomp.

The following external dependencies are distributed with NeEDL and do not have to be installed separately:

• Boost (version 1.71.0).
• Catch (version 2.13.9)
• CLI11 (version 1.9.0)
• Eigen (version 3.3.7)
• igraph (version 0.9.8)
• RapidJSON (version 1.1.0)

Building the tools

The first time, install.py will also compile and set up the dependencies in the ext/ and data/ folders.

# clone this repo
git clone https://github.com/biomedbigdata/NeEDL.git NeEDL
cd NeEDL

# get usage and available build targets
./install.py --help

# build only NeEDL (this sould be sufficient for most users)
./install.py --target NeEDL

# alternatively build all targets (might need additional dependencies)
./install.py --all-targets
# or build a different target
./install.py --target <target>

If the installation routine does not find the (correct) location for Python or the gcc compiler, one can specify the paths manually:

./install.py ... --python3 <path> --gcc <path> --gxx <path>

Per default, the dependencies are only compiled when using ./install.py the first time. To recompile the dependencies before the build use the following flag:

.install.py ... --clean

The final binaries can be found at ./test/model/bin.

Additional parameters

All of the parameters documented in the section Usage (Docker container) can be used analogously. Some additional parameters are necessary when using one of the tools outside the docker container. The parameters mentioned in this section are not necessary (and not allowed) to be used with the docker container.

# for NeEDL, calculate_scores and epiJSON:
# Either run NeEDL with cwd set to the root of the repo or pass this parameter specifing the path to the data/ directory of the repo (must end with a /).
--data-directory <path>

# for epiJSON:
# Either run NeEDL with cwd set to the root of the repo or pass this parameter specifing the path to the ext/ directory of the repo (must end with a /).
--ext-directory <path>