install

#!/bin/bash
#
# Install dependencies
#
# ** Must manually install conda first. **
# This script will create two conda environments (Python 2 and 3)
# and install dependencies to them.
# https://docs.conda.io/en/latest/miniconda.html
# https://repo.anaconda.com/miniconda/Miniconda2-latest-Linux-x86_64.sh
#
# ** Must manually download the IRIS_data set **
# https://drive.google.com/file/d/1TaswpWPnEd4TXst46jsa9XSMzLsbzjOQ/view?usp=sharing
#
# ** Must manually download IEDB tools version 2.15.5 to the IEDB directory. **
# download file to IEDB/IEDB_MHC_I-2.15.5.tar.gz
# This script will unpack and install the IEDB tools.
# http://tools.iedb.org/main/download/ -> MHC Class I -> previous version -> 2.15.5

function install_iedb() {
  echo
  echo "checking IEDB dependency"

  cd "${SCRIPT_DIR}/IEDB" || return 1

  if [[ ! -d mhc_i ]]
  then
    tar -xvf IEDB_MHC_I-2.15.5.tar.gz || return 1
  fi

  cd mhc_i || return 1

  ./configure || return 1
}

# This script will automatically download and build bedtools
# https://github.com/arq5x/bedtools2/releases
function install_bedtools() {
  echo
  echo "checking bedtools dependency"

  cd "${SCRIPT_DIR}" || return 1

  if [[ ! -d bedtools ]]
  then
    mkdir bedtools || return 1
  fi

  cd bedtools || return 1

  if [[ ! -f bedtools-2.29.0.tar.gz ]]
  then
    local BEDTOOLS_URI="https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz"
    curl -L "${BEDTOOLS_URI}" -o bedtools-2.29.0.tar.gz || return 1
  fi

  if [[ ! -d bedtools2 ]]
  then
    tar -xvf bedtools-2.29.0.tar.gz || return 1
  fi

  cd bedtools2 || return 1
  make || return 1
}

function install_star() {
  echo
  echo "checking STAR dependency"

  cd "${SCRIPT_DIR}" || return 1

  if [[ ! -d STAR ]]
  then
    mkdir STAR || return 1
  fi

  cd STAR || return 1

  if [[ ! -f 2.5.3a.tar.gz ]]
  then
    local STAR_URI="https://github.com/alexdobin/STAR/archive/2.5.3a.tar.gz"
    curl -L "${STAR_URI}" -o 2.5.3a.tar.gz || return 1
  fi

  if [[ ! -d STAR-2.5.3a ]]
  then
    tar -xvf 2.5.3a.tar.gz || return 1
  fi

  cd STAR-2.5.3a/source || return 1
  make || return 1
}

function install_samtools() {
  echo
  echo "checking SAM tools dependency"

  cd "${SCRIPT_DIR}" || return 1

  if [[ ! -d samtools ]]
  then
    mkdir samtools || return 1
  fi

  cd samtools || return 1

  if [[ ! -f samtools-1.3.tar.bz2 ]]
  then
    local SAMTOOLS_URI="https://sourceforge.net/projects/samtools/files/samtools/1.3/samtools-1.3.tar.bz2/download"
    curl -L "${SAMTOOLS_URI}" -o samtools-1.3.tar.bz2 || return 1
  fi

  if [[ ! -d samtools-1.3 ]]
  then
    tar -xvf samtools-1.3.tar.bz2 || return 1
  fi

  cd samtools-1.3 || return 1
  ./configure --enable-plugins --enable-libcurl --with-plugin-path="$(pwd)"/htslib-1.3 || return 1
  make all plugins-htslib || return 1
}

function install_rmats() {
  echo
  echo "checking rMATS dependency"

  cd "${SCRIPT_DIR}" || return 1

  if [[ ! -d rMATS ]]
  then
    mkdir rMATS || return 1
  fi

  cd rMATS || return 1

  if [[ ! -f rMATS.4.0.2.tgz ]]
  then
    local RMATS_URI="https://sourceforge.net/projects/rnaseq-mats/files/MATS/rMATS.4.0.2.tgz/download"
    curl -L "${RMATS_URI}" -o rMATS.4.0.2.tgz || return 1
  fi

  if [[ ! -d rMATS.4.0.2 ]]
  then
    tar -xvf rMATS.4.0.2.tgz || return 1
  fi
}

function install_cufflinks() {
  echo
  echo "checking Cufflinks dependency"

  cd "${SCRIPT_DIR}" || return 1

  if [[ ! -d cufflinks ]]
  then
    mkdir cufflinks || return 1
  fi

  cd cufflinks || return 1

  if [[ ! -f cufflinks-2.2.1.Linux_x86_64.tar.gz ]]
  then
    local CUFFLINKS_URI="http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-2.2.1.Linux_x86_64.tar.gz"
    curl "${CUFFLINKS_URI}" -o cufflinks-2.2.1.Linux_x86_64.tar.gz || return 1
  fi

  if [[ ! -d cufflinks-2.2.1.Linux_x86_64 ]]
  then
    tar -xvf cufflinks-2.2.1.Linux_x86_64.tar.gz || return 1
  fi
}

function install_seq2hla() {
  echo
  echo "checking seq2HLA dependency"

  cd "${SCRIPT_DIR}" || return 1

  if [[ ! -d seq2hla ]]
  then
    local SEQ_2_HLA_URI="https://bitbucket.org/sebastian_boegel/seq2hla"
    hg clone "${SEQ_2_HLA_URI}" || return 1
  fi
}

function install_ms_gf() {
  echo
  echo "checking MS GF+ dependency"

  cd "${SCRIPT_DIR}" || return 1

  if [[ ! -d ms_gf_plus ]]
  then
    mkdir ms_gf_plus || return 1
  fi

  cd ms_gf_plus || return 1

  if [[ ! -f MSGFPlus_v20190703.zip ]]
  then
    local MSGF_URI="https://github.com/MSGFPlus/msgfplus/releases/download/v2019.07.03/MSGFPlus_v20190703.zip"
    curl -L "${MSGF_URI}" -o MSGFPlus_v20190703.zip || return 1
  fi

  if [[ ! -f README.md ]]
  then
    unzip MSGFPlus_v20190703.zip || return 1
  fi
}

function install_python_packages() {
  echo
  echo "checking python dependencies"

  cd "${SCRIPT_DIR}" || return 1

  # Python 2
  conda::activate_env "${CONDA_ENV_NAME_2}" || return 1
  pip install -r requirements.txt || return 1
  conda install -c bioconda bowtie # has an error return even when successful
  conda::deactivate_env || return 1

  # Python 3
  conda::activate_env "${CONDA_ENV_NAME_3}" || return 1
  pip install -r qsub/requirements.txt || return 1
  conda::deactivate_env || return 1
}

function install_iris_data() {
  echo
  echo "checking IRIS data dependency"

  cd "${SCRIPT_DIR}" || return 1

  if [[ ! -d IRIS_data ]]
  then
    if [[ ! -f IRIS_data.tgz ]]; then
      echo "Need to download IRIS_data.tgz from:"
      echo "https://drive.google.com/file/d/1TaswpWPnEd4TXst46jsa9XSMzLsbzjOQ/view?usp=sharing"
      return 1
    fi

    tar -xvf IRIS_data.tgz || return 1
  fi
}

function install_iris_package() {
  echo
  echo "installing IRIS"

  cd "${SCRIPT_DIR}" || return 1

  conda::activate_env "${CONDA_ENV_NAME_2}" || return 1

  python setup.py install || return 1

  cd "${SCRIPT_DIR}" || return 1

  conda::deactivate_env || return 1
}


function ensure_conda_envs() {
  echo
  echo "checking conda"

  conda::create_env_with_name_and_python_version "${CONDA_ENV_NAME_2}"\
                                                 "${CONDA_PYTHON_VERSION_2}" || return 1

  conda::create_env_with_name_and_python_version "${CONDA_ENV_NAME_3}"\
                                                 "${CONDA_PYTHON_VERSION_3}" || return 1
}

function install_optional() {
  install_star
  if [[ "$?" -ne 0 ]]; then
    echo "Error installing optional dependency: star" >&2
  fi
  install_samtools
  if [[ "$?" -ne 0 ]]; then
    echo "Error installing optional dependency: samtools" >&2
  fi
  install_rmats
  if [[ "$?" -ne 0 ]]; then
    echo "Error installing optional dependency: rmats" >&2
  fi
  install_cufflinks
  if [[ "$?" -ne 0 ]]; then
    echo "Error installing optional dependency: cufflinks" >&2
  fi
  install_seq2hla
  if [[ "$?" -ne 0 ]]; then
    echo "Error installing optional dependency: seq2hla" >&2
  fi
  install_ms_gf
  if [[ "$?" -ne 0 ]]; then
    echo "Error installing optional dependency: ms gf" >&2
  fi
}

function install() {
  local INSTALL_OPTIONAL="$1"

  ensure_conda_envs || return 1

  install_iedb || return 1
  install_bedtools || return 1

  if [[ "${INSTALL_OPTIONAL}" -ne 0 ]]; then
    install_optional || return 1
  fi

  install_python_packages || return 1
  install_iris_data || return 1
  install_iris_package || return 1
}

function display_usage() {
  echo "usage:"
  echo "  ./install {core|all}"
  echo ""
  echo "./install core: installs only the required dependencies for the major IRIS modules"
  echo ""
  echo "./install all: installs all dependencies"
}

function main() {
  local INSTALL_OPTIONAL

  if [[ "$#" -ne 1 ]]; then
    echo "exactly one argument required" >&2
    display_usage
    return 1
  elif [[ "$1" = 'core' ]]; then
    INSTALL_OPTIONAL=0
  elif [[ "$1" = 'all' ]]; then
    INSTALL_OPTIONAL=1
  else
    echo "unrecognized argument: $1" >&2
    display_usage
    return 1
  fi

  source set_env_vars.sh || return 1
  source conda.sh || return 1

  SCRIPT_DIR="$(pwd)" || return 1

  install "${INSTALL_OPTIONAL}" || return 1
}

main "$@"