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Installation.md

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Installation of Paragraph

System Requirements

Hardware

A standard workstation with at least 8GB of RAM should be sufficient for compilation and testing of the program.

Operating systems

Paragrpah is supported on the following systems:

  • Ubuntu 16.04 and CentOS 5-7,
  • macOS 10.11+,

Python 3.6+ is required.

We recommend using g++ (6.0+), or a recent version of Clang.

We use the C++11 standard, any Posix compliant compiler supporting this standard should be usable.

Third-party libraries

Please check requirements for required python modules.

We have included copies of other dependent libraries in external/. They are:

  • Google Test and Google Mock (v1.8.0)
  • Htslib (v1.9)
  • Spdlog

Static Build

We provide a static build that works for GCC 5.2+ under linux environment. No installation is required for the static build.

Download the static build under "release" tag of the github repo.

Installation

Native buid

Boost libraries version >= 1.5 is required.

  • We prefer to statically link Boost libraries to Paragraph executables:

    cd ~
wget http://downloads.sourceforge.net/project/boost/boost/1.65.0/boost_1_65_0.tar.bz2
tar xf boost_1_65_0.tar.bz2
cd boost_1_65_0
./bootstrap.sh
./b2 --prefix=$HOME/boost_1_65_0_install link=static install

  • To point Cmake to your version of Boost use the BOOST_ROOT environment variable:

    export BOOST_ROOT=$HOME/boost_1_65_0_install

Once you have boost installed, checkout the repository like so:

git clone https://github.com/Illumina/paragraph.git
cd paragraph-tools

Then create a new directory for the program and compile it there:

# Create a separate build folder.
cd ..
mkdir paragraph-tools-build
cd paragraph-tools-build

# Configure
# optional:
# export BOOST_ROOT=<path-to-boost-installation>
cmake ../paragraph-tools
# if this doesn't work, run this instead:
# cmake ../paragraph-tools -DCMAKE_CXX_COMPILER=`which g++` -DCMAKE_C_COMPILER=`which gcc` -DBOOST_ROOT=$BOOST_ROOT

# Make, use -j <n> to use n parallel jobs to build, e.g. make -j4
make

From Docker Image

We also provide a Dockerfile. To build a Docker image, run the following command inside the source checkout folder:

docker build .

Once the image is built you can find out its ID like this:

docker images
REPOSITORY                             TAG                 IMAGE ID            CREATED             VIRTUAL SIZE
<none>                                 <none>              54c7d4015330        16 seconds ago      1.76 GB

Check the below section for how to run Paragraph, and execute this before running:

sudo docker run -v `pwd`:/data 54c7d4015330

The current directory can be accessed as /data inside the Docker container.

The default entry point is multigrmpy.py.

To override the default entrypoint and get an interactive shell, run:

sudo docker run --entrypoint /bin/bash -it 54c7d4015330