setup.sh

#!/bin/bash
#Note users will require a github account and need to have virtualenv installed


setup(){

  mkdir ./Dropseq_Alignment_Cookbook
  cd Dropseq_Alignment_Cookbook
  wget http://mccarrolllab.com/download/1276/Drop-seq_tools-1.13-3.zip
  unzip Drop-seq_tools-1.13-3.zip
  mkdir temp_files
  wget https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.9.0/sratoolkit.2.9.0-ubuntu64.tar.gz
  tar -xvzf sratoolkit.2.9.0-ubuntu64.tar.gz
  wget https://github.com/broadinstitute/picard/releases/download/2.18.0/picard.jar
  cd ..


  #First make a directory in which simulation data and programs will be kept
  mkdir ./Simulation

  #Install programs in directory
  cd Simulation

  #Install RSEM
  wget https://github.com/deweylab/RSEM/archive/v1.3.0.tar.gz
  tar -xvzf v1.3.0.tar.gz
  rm v1.3.0.tar.gz
  cd RSEM
  make
  make install prefix=.
  cd ..
  if ! command -v ./RSEM/rsem-generate-data-matrix >/dev/null 2>&1; then
    echo "Failed to install RSEM"
    exit 1
  else
    echo "Successfully installed RSEM"
  fi

  #Fix bug in RSEM (see https://github.com/deweylab/RSEM/pull/79)
  git clone https://github.com/jenni-westoby/RSEM.git
  cp RSEM/simul.h RSEM/simul.h
  rm -r RSEM

  #Install Sailfish
  wget https://github.com/kingsfordgroup/sailfish/releases/download/v0.10.0/SailfishBeta-0.10.0_CentOS5.tar.gz
  tar -xvzf SailfishBeta-0.10.0_CentOS5.tar.gz
  rm SailfishBeta-0.10.0_CentOS5.tar.gz
  export LD_LIBRARY_PATH=`pwd`/SailfishBeta-0.10.0_CentOS5/lib:$LD_LIBRARY_PATH
  export PATH=`pwd`/SailfishBeta-0.10.0_CentOS5/bin:$PATH
  if ! command -v ./SailfishBeta-0.10.0_CentOS5/bin/sailfish -h; then
    echo "Failed to install Sailfish"
    exit 1
  else
    echo "Successfully installed Sailfish"
  fi

  #Install eXpress
  wget https://pachterlab.github.io/eXpress/downloads/express-1.5.1/express-1.5.1-linux_x86_64.tgz
  tar -xvzf express-1.5.1-linux_x86_64.tgz
  rm express-1.5.1-linux_x86_64.tgz
  if ! command -v ./express-1.5.1-linux_x86_64/express >/dev/null 2>&1; then
    echo "Failed to install eXpress"
    exit 1
  else
    echo "Successfully installed eXpress"
  fi

  #Install Salmon
  wget https://github.com/COMBINE-lab/salmon/releases/download/v0.8.2/Salmon-0.8.2_linux_x86_64.tar.gz
  tar -xvzf Salmon-0.8.2_linux_x86_64.tar.gz
  rm Salmon-0.8.2_linux_x86_64.tar.gz
  if ! command -v ./Salmon-0.8.2_linux_x86_64/bin/salmon >/dev/null 2>&1; then
    echo "Failed to install Salmon"
    exit 1
  else
    echo "Successfully installed Salmon"
  fi

  #Install Kallisto
  wget https://github.com/pachterlab/kallisto/releases/download/v0.43.1/kallisto_linux-v0.43.1.tar.gz
  tar -xvzf kallisto_linux-v0.43.1.tar.gz
  rm kallisto_linux-v0.43.1.tar.gz
  if ! command -v ./kallisto_linux-v0.43.1/kallisto >/dev/null 2>&1; then
    echo "Failed to install Kallisto"
    exit 1
  else
    echo "Successfully installed Kallisto"
  fi

  #Install STAR
  git clone https://github.com/alexdobin/STAR.git
  if ! command -v ./STAR/bin/Linux_x86_64/STAR >/dev/null 2>&1; then
    echo "Failed to install STAR"
    exit 1
  else
    echo "Successfully installed STAR"
  fi

  #Install samtools
  wget https://github.com/samtools/samtools/releases/download/1.5/samtools-1.5.tar.bz2
  bzip2 -d samtools-1.5.tar.bz2
  tar -xvf samtools-1.5.tar
  rm samtools-1.5.tar
  cd samtools-1.5/
  ./configure --prefix=`pwd`
  make
  make install
  cd ..
  if ! command -v ./samtools-1.5/samtools >/dev/null 2>&1; then
    echo "Failed to install SAMtools"
    exit 1
  else
    echo "Successfully installed SAMtools"
  fi

  #Get drop-seq data
  ../Dropseq_Alignment_Cookbook/sratoolkit.2.9.0-ubuntu64/bin/prefetch SRR3587500
  ../Dropseq_Alignment_Cookbook/sratoolkit.2.9.0-ubuntu64/bin/sam-dump SRR3587500.sra | ./samtools-1.5/samtools view -bS -> ../Dropseq_Alignment_Cookbook/SRR3587500.bam

  #Install virtualenv and RSeQC
  git clone https://github.com/pypa/virtualenv.git
  python virtualenv/virtualenv.py venv
  source venv/bin/activate
  pip install RSeQC
  if ! command -v  >/dev/null 2>&1; then
    echo "Failed to install RSeQC"
    exit 1
  else
    echo "Successfully installed RSeQC"
  fi

  #Make a directory for RNA-seq data including raw and simulated data
  mkdir data
  cd data
  mkdir simulated
  mkdir temp
  cd ..

  #Make a directory for quality control statistics for raw and simulated data
  mkdir QC_stats
  cd QC_stats
  mkdir raw
  mkdir simulated
  mkdir temp_raw
  mkdir temp_simulated
  cd ..

  mkdir indices
  mkdir indices/STAR
  mkdir indices/Salmon_SMEM
  mkdir indices/Salmon_quasi
  mkdir indices/Kallisto
  mkdir indices/Sailfish

  mkdir bamfiles
  mkdir bamfiles/raw
  mkdir bamfiles/simulated

  mkdir time_stats

  mkdir ref
  mkdir results_matrices

  mkdir raw_results/data
  
  mkdir figures/data
  mkdir figures/pdfs
  mkdir figures/pngs

}

"$@"