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Installation
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Installing HTStream version 1.2.0

Install binaries for linux systems:

On Linux systems, the easiest and most straight forward option is to download and unpack the pre-compiled binaries to somewhere on your $PATH.

wget https://github.com/ibest/HTStream/releases/download/v1.2.0-release/HTStream_v1.2.0-release.tar.gz

tar xvf HTStream_v1.2.0-release.tar.gz

Install from Bioconda:

HTStream is available through the Bioconda channel. Visit Miniconda.

conda install -c bioconda htstream

Compiling HTStream from source

Prerequisites:

  • Cmake 3.2 or greater.
  • GCC 4.8 - 4.9.x or >= 5.3 (or Clang 3.3 or greater)
  • Boost 1.56 or greater including the following
    • libboost-dev
    • libboost-system-dev
    • libboost-program-options-dev
    • libboost-iostreams-dev
    • libboost-filesystem-dev

On Debian based systems (e.g. Ubuntu) prerequisites can be installed as follows

sudo apt-get install cmake
sudo apt install libboost-dev libboost-system-dev libboost-program-options-dev libboost-iostreams-dev libboost-filesystem-dev

on Mac OSX using Homebrew

brew upgrade
brew install cmake
brew install boost

Alternatively Boost can be installed from source:

wget https://dl.bintray.com/boostorg/release/1.65.1/source/boost_1_65_1.tar.bz2
tar --bzip2 -xf boost_1_65_1.tar.bz2
cd boost_1_65_1
./bootstrap.sh
./b2
BOOST_INCLUDE=$(pwd)
BOOST_INCLUDE_LIB=$(pwd)/stage/lib

Compiling HTStream from source

Downloading the current release version

wget -O HTStream-v1.3.1-release.zip https://github.com/ibest/HTStream/archive/v1.3.1-release.zip
unzip HTStream-v1.3.1-release.zip
cd HTStream-1.3.1-release

OR Downloading the current development version

git clone https://github.com/ibest/HTStream.git
cd HTStream

Compiling the source code with cMake and make

mkdir build
cd build
cmake ..
make
make test
make install

default install prefix is /usr/local/bin which may require super user or sudo access {:.danger}

Optional cmake parameters

When using an alternative Boost install location

cmake -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB ..

To specify an different install prefix

cmake -DCMAKE_INSTALL_PREFIX=/path/to/install ..

Building binaries with statically linked libraries

cmake -DBUILD_STATIC_BIN=ON ..

Troubleshooting

Some users have experienced issues with the boost install. We think this arises from having other versions of boost on the system. Try the following:

cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DBOOST_INCLUDEDIR=/usr/local/include/ ..

Or try

export CC=`which gcc`
export CXX=`which g++`
mkdir -p build
cd build
cmake -DBoost_NO_SYSTEM_PATHS=TRUE -DCMAKE_INCLUDE_PATH=$BOOST_INCLUDE -DCMAKE_LIBRARY_PATH=$BOOST_INCLUDE_LIB ..
make
make test
make install