installer

#!/bin/bash
# This script installs PyDesigner and all dependencies within
# Debian-based systems
# Author: Siddhartha Dhiman
#
# Note:
#   The scipt will ask for root password if not run by root user

# Declate predefined variables
ISFSL=0
ISMRTRIX=0
ISPYD=0
FSLINSTALL=/usr/local/fsl
MRTRIXINSTALL=/usr/local/mrtrix3
RED='\033[0;31m'
GREEN='\033[32m'
NC='\033[0m'


# Install dependencies
sudo apt-get update && \
    sudo apt-get install -y \
        apt-utils \
        wget \
        curl \
        nano \
        software-properties-common \
        python2.7 python-pip \
        python3 python3-pip \
        jq

sudo apt-get install -y --no-install-recommends \
    clang \
    git \
    python-numpy \
    libeigen3-dev \
    zlib1g-dev \
    libqt4-opengl-dev \
    libgl1-mesa-dev \
    libfftw3-dev \
    libtiff5-dev \
    libomp-dev

# Check installation of FSL, MRtrix3 and PyDesigner
if [[ $(echo $FSLDIR) ]]; then
    echo -e "${GREEN}Existing FSL installation found${NC}\n"
    ISFSL=1
else
    echo -e "${RED}FSL installation not found...marked for installation\n${NC}"
    ISFSL=0
fi

if [[ $(which dwipreproc) ]]; then
    echo -e "${GREEN}Existing MRtrix3 installation found\n${NC}"
    ISMRTRIX=1
else
    echo -e "${RED}MRtrix3 installation not found...marked for installation\n${NC}"
    ISMRTRIX=0
fi

if [[ $(which pydesigner) ]]; then
    echo -e "${GREEN}Existing PyDesigner installation found\n${NC}"
    ISPYD=1
else
    echo -e "${RED}PyDesigner installation not found...marked for installation\n${NC}"
    ISPYD=0
fi

# Install PyDesigner
if [ "$ISPYD" -eq "0" ]; then
    sudo mkdir -p /tmp/PyDesigner
    export PYDVER=$(curl -s https://api.github.com/repos/m-ama/PyDesigner/releases | jq -r '.[0] | .tag_name')
    export URL=$(curl -s https://api.github.com/repos/m-ama/PyDesigner/releases | jq -r '.[0] | .tarball_url')
    echo -e "${NC}Installing PyDesigner $PYDVER${NC}"
    sudo wget -q -O - $URL | sudo tar -xzf - -C /tmp/PyDesigner --strip 1
    sudo pip3 install /tmp/PyDesigner
    sudo rm -r /tmp/PyDesigner
else
    :
fi

# Install FSL
if [ "$ISFSL" -eq "0" ]; then
    echo -e "${NC}Installing FSL${NC}"
    curl https://fsl.fmrib.ox.ac.uk/fsldownloads/fslinstaller.py -o /tmp/fslinstaller.py
    sudo echo $FSLINSTALL| python2 /tmp/fslinstaller.py -V 6.0.3
    sudo echo 'export FSLDIR=/usr/local/fsl' >> ~/.bashrc
    sudo echo 'export FSLOUTPUTTYPE=NIFTI_GZ' >> ~/.bashrc
    sudo echo 'export PATH=$PATH:$FSLDIR/bin' >> ~/.bashrc
    sudo echo 'export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$FSLDIR' >> ~/.bashrc
else
    :
fi

# Install MRtrix3
if [ "$ISMRTRIX" -eq "0" ]; then
    echo -e "${NC}Installing MRTrix3${NC}"
    sudo git clone https://github.com/MRtrix3/mrtrix3.git /usr/local/mrtrix3
    CXX=/usr/bin/clang++
    ARCH=native
    ./usr/local/mrtrix3/configure && \
        ./usr/local/mrtrix3/build && \
        ./usr/local/mrtrix3/set_path
    sudo echo 'export PATH=$PATH:/usr/local/mrtrix3/bin' >> ~/.bashrc
else
    :
fi

source ~/.bashrc
echo -e "${GREEN}Installation Complete"
echo -e "Please close this Terminal window and reopen a new window for"
echo -e "changes to take effect\n${NC}"