# Environment: Linux 64 bits
# The tools are tested on Linux Mint 19 - Tara, 64bit. and Ubuntu 18.04

# 0. Install JAVA if you don't have it already
sudo apt install default-jre

# 1. Download fastqc
mkdir -p ~/Downloads/bin
cd ~/Downloads/bin 
wget https://www.bioinformatics.babraham.ac.uk/projects/fastqc/fastqc_v0.11.8.zip
unzip fastqc_v0.11.8.zip
rm fastqc_v0.11.8.zip
# make sure that fastqc is executable
sudo chmod 770 FastQC/fastqc

# 2. Download trim galore
cd ~/Downloads/bin
wget https://github.com/FelixKrueger/TrimGalore/archive/0.6.0.zip
unzip 0.6.0.zip
rm 0.6.0.zip

# 3. Install samtools
sudo apt install samtools # For Ubuntu-based distributions

# 4. Install python3.6 and pip
# check if you already have it installed with 
python3 --version
# if not run
# sudo apt install python3.6
sudo apt install python3-pip
pip3 install --user --upgrade cutadapt
# Also set ~/.local/bin to be part of your PATH in the .bashrc file.
# Add:     export PATH=/home/$USER/.local/bin:$PATH     to ~/.bashrc file
# 

# 5. Install STAR aligner
cd ~/Downloads/bin
wget https://github.com/alexdobin/STAR/archive/master.zip
unzip master.zip
# you will also need some dependencies
sudo apt install zlib1g-dev
cd STAR-master/source
make STAR
# install missing dependencies if any discovered during installation

# 6. Install IGV (2.4.9)
cd ~/Downloads/bin
wget http://data.broadinstitute.org/igv/projects/downloads/2.5/IGV_Linux_2.5.0.zip
unzip IGV_Linux_2.5.0.zip
rm IGV_Linux_2.5.0.zip

# 7. Install newest R and R-Studio
sudo apt install apt-transport-https software-properties-common libclang-dev libcurl4-openssl-dev libssl-dev
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
sudo add-apt-repository 'deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/'
sudo apt update
sudo apt install r-base
wget https://download1.rstudio.org/desktop/bionic/amd64/rstudio-1.2.1335-amd64.deb
sudo dpkg -i rstudio-1.2.1335-amd64.deb
# Install missing dependencies in linux (if any)
# from R install additional packages 
R
> install.packages("dplyr")
> install.packages("devtools")
> devtools::install_github("satijalab/seurat", ref = "develop")