README.md

In cytolib: C++ infrastructure for representing and interacting with the gated cytometry data

C++ library for the gated cytometry data

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 the c++ library for users to use and interact with the GatingSet (the gated cytometry data structure) at c++ level.

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.

Install tiledb (optional)

When tiledb library is detected from the system, cytolib will try to build against it so that tiledb can be used as the alternative backend format. To build tiledb from source:

Download source

git clone https://github.com/TileDB-Inc/TileDB --depth=1 --branch=dev --single-branch
cd TiledB
mkdir build
cd build

Install to the default system location (i.e. /usr/local)

../bootstrap --enable-s3
make
sudo make install-tiledb

Or install to the custom location (e.g. /home/mypath)

../bootstrap --prefix=/home/mypath --enable-s3
make
make install-tiledb

Installation cytolib as a R package

The cytolib package can be installed from Github

    remotes::install_github("RGLab/cytolib")

If the TileDB library is installed in a custom location,make sure its library path is added to the runtime path.i.e.

export LD_LIBRARY_PATH=/home/mypath/lib:$LD_LIBRARY_PATH

and you also need to pass the explicit path:

remotes::install_github("RGLab/cytolib",
    args="--configure-args='--with-tiledb=/home/mypath'")

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

Installation

# 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 tiledb that is installed at custom location
# e.g. `cmake -DCMAKE_PREFIX_PATH=</path/to/TileDB>`

# 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

cytolib documentation built on Jan. 19, 2021, 2 a.m.