Requirements

If you are not in sudoers, then you can still install AMO without root access. Firstly, you are required to install the dependencies step by step.

Unix-like system

sudo apt-get update
sudo apt-get install -y --no-install-recommends \
      build-essential \
      libgflags-dev \
      libgoogle-glog-dev \
      libomp-dev \
      libeigen3-dev \
      libbz2-dev \
      libhdf5-dev

Mac OSX

We highly recommend using the Homebrew package manager to install the dependencies.

brew install -vd cmake gflags glog boost
brew install zlib bzip2

Step-by-step

GCC

Sometimes, on an old UNIX-like distribution, a new version of gcc is required (i.e. utilize the features from C++11 standard) before installing other dependencies. Don't worry, here is how you can compile your own gcc on the distribution with/without root access.

#! /bin/bash
set -e
#-----------------------------------------------------------------------------
# This script, as part of AMO, will download packages, configure, 
# build and install GCC, Make, Cmake on Unix-like systems. Customize the 
# variables (GCC_VERSION, MAKE_VERSION, etc.) before running.
# Copyright@2017, AMO AI
# Email: [e-mail]
#-----------------------------------------------------------------------------

# Path where to install without root
LOCAL_PATH=/home/<username>/local

# Customize the versions
PARALLEL_MAKE=-j128
GCC_VERSION=gcc-6.3.0
MPFR_VERSION=mpfr-3.1.5
GMP_VERSION=gmp-6.1.2
MPC_VERSION=mpc-1.0.3
MAKE_VERSION=make-4.2
CMAKE_VERSION=cmake-3.12.2

# Creat a directory
if [ ! -f amo-gnu ]; then
  mkdir -p amo-gnu
else
  rm -rf amo-gnu
fi
cd amo-gnu/


# Download packages, maybe you already have the packages, please put them in the directory <amo-gnu>
export http_proxy=$HTTP_PROXY https_proxy=$HTTP_PROXY ftp_proxy=$HTTP_PROXY
wget -nc https://ftp.gnu.org/gnu/gmp/$GMP_VERSION.tar.xz
wget -nc https://ftp.gnu.org/gnu/mpfr/$MPFR_VERSION.tar.xz
wget -nc https://ftp.gnu.org/gnu/mpc/$MPC_VERSION.tar.gz
wget -nc https://ftp.gnu.org/gnu/gcc/$GCC_VERSION/$GCC_VERSION.tar.gz
wget -nc http://ftp.gnu.org/gnu/make/$MAKE_VERSION.tar.gz
wget -nc https://cmake.org/files/v3.12/cmake-3.12.2.tar.gz

# Extract Packages
echo "Extracting tar files ..."
for f in *.tar*; do tar xfk $f; done

# Step 1. Install GMP
echo "Step 1. Installing GMP ..."
cd $GMP_VERSION
mkdir build && cd build
../configure --prefix=$LOCAL_PATH/$GMP_VERSION --enable-cxx
nice -n 19 time make $PARALLEL_MAKE
make install && make check
cd ../..

# Step 2. Install MPFR
echo "Step 2. Installing MPFR ..."
cd $MPFR_VERSION
mkdir build && cd build
../configure --prefix=$LOCAL_PATH/$MPFR_VERSION --with-gmp=$LOCAL_PATH/$GMP_VERSION 
nice -n 19 time make $PARALLEL_MAKE
make install && make check
cd ../..

# Step 3. Install MPC
echo "Step 3. Installing MPC ..."
cd $MPC_VERSION
mkdir build && cd build
LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib \
../configure --prefix=$LOCAL_PATH/$MPC_VERSION \
--with-gmp=$LOCAL_PATH/$GMP_VERSION \
--with-mpfr=$LOCAL_PATH/$MPFR_VERSION
LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib \
nice -n 19 time make $PARALLEL_MAKE
make install && make check
cd ../..

# Step 4. Install GCC
echo "Step 4. Installing GCC ..."
cd $GCC_VERSION
mkdir -p build && cd build
LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib \
../configure --prefix=$LOCAL_PATH/$GCC_VERSION \
--with-gmp=$LOCAL_PATH/$GMP_VERSION \
--with-mpfr=$LOCAL_PATH/$MPFR_VERSION \
--with-mpc=$LOCAL_PATH/$MPC_VERSION \
--disable-multilib \
--enable-languages=c,c++ \
--enable-libgomp
LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib \
nice -n 19 time make $PARALLEL_MAKE
make install && make check
cd ../..

## Step 5. Install Make
#echo "Step 5. Installing Make ..."
#cd $MAKE_VERSION
#mkdir -p build && cd build
#LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib \
#../configure --prefix=$LOCAL_PATH/$MAKE_VERSION
#LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib \
#nice -n 19 time make $PARALLEL_MAKE
#make install && make check
#cd ../..

## Step 6. Install Make
#echo "Step 6. Installing Cmake ..."
#cd $CMAKE_VERSION
#mkdir -p build && cd build
#LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib64:$LOCAL_PATH/$MAKE_VERSION/lib \
#../configure --prefix=$LOCAL_PATH/$CMAKE_VERSION
#LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib64:$LOCAL_PATH/$MAKE_VERSION/lib \
#nice -n 19 time make $PARALLEL_MAKE
#make install && make check
#cd ../..

## echo $MACHTYPE
##$LOCAL_PATH/$GCC_VERSION/lib64 is correct on x86_64; it may need to be replaced with $LOCAL_PATH/$GCC_VERSION/lib on other platforms.
## Or paste the following lines to ~/.bashrc in Unix-like systems
export LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib64:$LOCAL_PATH/$MAKE_VERSION/lib:$LOCAL_PATH/$CMAKE_VERSION/lib
export PATH=$LOCAL_PATH/$GCC_VERSION/bin:$PATH
#export PATH=$LOCAL_PATH/$MAKE_VERSION/bin:$PATH
#export PATH=$LOCAL_PATH/$CMAKE_VERSION/bin:$PATH

Make

If the version of gcc is not too old on your distribution, you can just simply install the make as follows,

wget -nc https://ftp.gnu.org/gnu/make/make-4.2.tar.gz
tar -xzvf make-4.2.tar.gz
./configure --prefix=/home/<username>/local
make
make install

If you compile your gcc own , then you are recommanded (as shown above in step 5, just uncomment the lines) to run as follows,

## Step 5. Install Make
# echo "Step 5. Installing Make ..."
cd $MAKE_VERSION
mkdir -p build && cd build
LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib \
../configure --prefix=$LOCAL_PATH/$MAKE_VERSION
LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib \
nice -n 19 time make $PARALLEL_MAKE
make install && make check
cd ../..
# !important, add the line into ~/.bashrc
export PATH=$LOCAL_PATH/$MAKE_VERSION/bin:$PATH

Cmake

wget -nc https://cmake.org/files/v3.12/cmake-3.12.2.tar.gz
tar -xvf cmake-3.12.2.tar.gz
cd cmake-3.12.2
./configure --prefix=/home/<username>/local/
make && make install 
cmake --version 

Or install cmake by following lines if you compile your own gcc

## Step 6. Install Make
#echo "Step 6. Installing Cmake ..."
cd $CMAKE_VERSION
mkdir -p build && cd build
LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib64:$LOCAL_PATH/$MAKE_VERSION/lib \
../configure --prefix=$LOCAL_PATH/$CMAKE_VERSION
LD_LIBRARY_PATH=$LOCAL_PATH/$GMP_VERSION/lib:$LOCAL_PATH/$MPFR_VERSION/lib:$LOCAL_PATH/$MPC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib:$LOCAL_PATH/$GCC_VERSION/lib64:$LOCAL_PATH/$MAKE_VERSION/lib \
nice -n 19 time make $PARALLEL_MAKE
make install && make check
cd ../..

# !important, add the line into ~/.bashrc
export PATH=$LOCAL_PATH/$CMAKE_VERSION/bin:$PATH

Boost library

On Unix-like system, it is easy to install Boost library with sudo, type the following command in the terminal to install Boost library.

apt-get install libboost-all-dev

If you would like to install the Boost library without root, you can follow this instruction to install it.

wget -nc https://dl.bintray.com/boostorg/release/1.65.0/source/boost_1_65_0.tar.gz
tar -xvzf boost_1_65_0.tar.gz
cd boost_1_65_0                                             
./bootstrap.sh \
--libdir=/home/<username>/local/lib \
--includedir=/home/<username>/local/include
./b2                                                             
./b2 install  

Gflags

The gflags package contains a C++ library that implements command line flags processing.

The latest version of gflags is not validated for the AMO software.

wget -nc https://github.com/gflags/gflags/archive/v2.2.2.tar.gz
cd gflags
mkdir build
cd build
# ccmake # edit the prefix to /home/username/local, and type c
# or
cmake CMAKE_INSTALL_PREFIX=/home/<username>/local ..
vi CMakeCache.txt # edit CMAKE_CXX_FLAGS:STRING=-fPIC
make 
make install DESTDIR=/home/<username>/local

Glog

The glog library contains a C++ implementation of the Google logging module.

The latest version of glog is not validated for the AMO software.

wget -nc https://github.com/google/glog/archive/v0.4.0.tar.gz
tar -xvzf *.tar.gz
./configure --prefix=/home/<username>/local
make 
make install

HDF5

AMO is only tested on HDF5 Version 1.8.14

PyTorch

More details can be found here. In AMO, we call modules in PyTorch to build deep learning models that are leveraged to analyze biological data.

git clone -b master --recurse-submodule https://github.com/pytorch/pytorch.git

mkdir pytorch-build

cd pytorch-build

cmake \
-DBUILD_SHARED_LIBS:BOOL=ON \
-DUSE_MKLDNN=ON \
-DUSE_MKLDNN_ACL=ON \
-DUSE_MKLDNN_CBLAS=ON \
-DCMAKE_BUILD_TYPE:STRING=Release \
-DPYTHON_EXECUTABLE:PATH=`which python3` \
../pytorch

#-DCMAKE_INSTALL_PREFIX:PATH=../pytorch-install 

make install

Plotting

If one would like to run amo with figures, plotting packages are required to install. Gnuplot and R are two packages to generate figures.

$ sudo apt install r-base

Then, install library circlize as follows,

install.packages("circlize")

Install Gnuplot in the terminal as follows,

$ sudo apt install gnuplot