Alfred documentation

# Installation

Alfred is available as a Bioconda package, as a pre-compiled statically linked binary from Alfred's github release page or as a minimal Docker container. All code is open-source and hosted on Alfred's GitHub page.

# Installation from Source

To build Alfred from source you need some build essentials and the Boost libraries, i.e. for Ubuntu:

apt install \
    build-essential g++ \
    cmake \
    git-all \
    liblzma-dev \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    libboost-date-time-dev \
    libboost-program-options-dev \
    libboost-system-dev \
    libboost-filesystem-dev \
    libboost-iostreams-dev

Once you have installed these system libraries you can compile and link Alfred.

git clone --recursive https://github.com/tobiasrausch/alfred.git
cd alfred/
make all
make install
./bin/alfred -h

# Custom Boost installation directory

Alfred requires Boost and you can install Boost locally using

git clone --recursive https://github.com/boostorg/boost.git
cd boost/
./bootstrap.sh --prefix=`pwd` --without-icu --with-libraries=iostreams,filesystem,system,program_options,date_time
./b2
./b2 headers
cd ..

You can then specify the custom Boost installation directory (i.e., /opt/boost below) using

# modify the following line accordingly
BOOSTROOT=/opt/boost
git clone --recursive https://github.com/tobiasrausch/alfred.git
cd alfred/
make CMDCXXFLAGS="-isystem $BOOSTROOT" CMDLDFLAGS="-L$BOOSTROOT/stage/lib -Wl,-rpath,$BOOSTROOT/stage/lib" all
make install
./bin/alfred -h

Usage →