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# C++ library for computational cytometry # License Copyright 2019, Fred Hutchinson Cancer Research Center See the included LICENSE file for details on the license granted to the user of this software. `cytolib` provides a c++ library for interacting with cytometry data. - reading FCS into efficient disk-backed and memory-backed data structures - representation of gated cytometry data. - core library backing the R packages flowCore, flowWorkspace, CytoML, and others that provide a high level R language interface. ### Reporting Bugs or Issues - Use the issue template in github when creating a new issue. - Follow the instructions in the template (do your background reading). - Search and verify that the issue hasn't already been addressed. - Check the Bioconductor support site. - Make sure your flow packages are up to date. - THEN if your issue persists, file a bug report. Otherwise, we may close your issue without responding. ## Installation cytolib as a R package The **cytolib** package can be installed from Github ``` remotes::install_github("RGLab/cytolib") ``` R packages wishing to use the libraries in `cytolib` need to: - add `cytolib` to **LinkingTo** field in the **DESCRIPTION** file so the compiler knows where to find the headers when the user package is complied e.g. ``` LinkingTo: cytolib ``` See **CytoML** package for the example of using `cytolib`. ## Installation as a C++ standalone library **System requirement** 1. cmake 2. g++ (>=4.9) or clang++(>= 7.0.1) 3. libblas, liblapack, ZLIB, boost c++ library 4. protobuf c++ library (>= 3.10) **Installation** ```bash # enter your project directory $ cd cytolib # it is always a good idea to not pollute the source with build files # so create a new build directory $ mkdir build $ cd build # run cmake to configure the package for your system $ cmake .. # to link against the protobuf that is installed at custom location # e.g. `cmake -DCMAKE_PREFIX_PATH=</path/to/protobuf>` # to select different compiler other than the default # e.g. `cmake -DCMAKE_CXX_COMPILER=clang++` #To install the library to custom directory, use `-DCMAKE_INSTALL_PREFIX` option # e.g. `cmake -DCMAKE_INSTALL_PREFIX=/usr/local` $ make #to install the package $ make install ```