script for building bcl2fastq2 2.20.0 on POSIX systems

build_bcl2fastq2_2_20_0.sh

#!/usr/bin/env zsh

# script to build Illumina bcl2fastq2 
# Copyright (C) 2017  Lior Galanti
# NYU Center for Genetics and System Biology

# Author: Lior Galanti <[email protected]>

# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU Affero General Public License as
# published by the Free Software Foundation, either version 3 of the
# License, or (at your option) any later version.

# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
# GNU Affero General Public License for more details.

# You should have received a copy of the GNU Affero General Public License
# along with this program.  If not, see <http://www.gnu.org/licenses/>.


# This script will build bcl2fastq2 version 2.20.0
# for some reason the source code provided by illumina seems to assume and older version 
# of boost on POSIX systems that where the boost::property_tree::xml_writer_make_settings
# function is not templatized and so fails to build against newer versions of boost on those platforms.

# a patch is available for correcting this silly assumption here: 
# https://gist.github.com/moonwatcher/ac1176971d6032fc9e0d4402e5a81333

BCL2FASTQ_WORK_DIRECTORY="$(cd ~ && pwd)/bcl2fastq_2_20_1_work_directory"
BCL2FASTQ_ARCHIVE_URL="ftp://webdata2:[email protected]/downloads/software/bcl2fastq/bcl2fastq2-v2-20-0-tar.zip"
BCL2FASTQ_ARCHIVE_URL_MD5="4dc99f1af208498b7279b66556329488"
BCL2FASTQ_ARCHIVE_LOCAL="$BCL2FASTQ_WORK_DIRECTORY/bcl2fastq2-v2-20-0-tar.zip"
BCL2FASTQ_BOOST_PATCH_URL="https://gist.githubusercontent.com/moonwatcher/ac1176971d6032fc9e0d4402e5a81333/raw"
BCL2FASTQ_BOOST_PATCH_MD5="5c887a6316d188f6e34dabe35f6be466"
BCL2FASTQ_BOOST_PATCH_LOCAL="$BCL2FASTQ_WORK_DIRECTORY/bcl2fastq2_2_20_0_xml_writer_make_settings.patch"

BCL2FASTQ_SOURCE="$BCL2FASTQ_WORK_DIRECTORY/bcl2fastq"
BCL2FASTQ_BUILD="$BCL2FASTQ_WORK_DIRECTORY/build"

# create work directory
if [[ ! -d "$BCL2FASTQ_WORK_DIRECTORY" ]]; then
  >&2 echo "creating work directory $BCL2FASTQ_WORK_DIRECTORY";
  mkdir -p "$BCL2FASTQ_WORK_DIRECTORY";
fi

check_archive() {
    local ARCHIVE_REMOTE_URL="$1";
    local ARCHIVE_LOCAL_URL="$2";
    local ARCHIVE_REMOTE_MD5="$3";

    if [[ -f "$ARCHIVE_LOCAL_URL" ]]; then
      local ARCHIVE_LOCAL_MD5=$(md5sum "$ARCHIVE_LOCAL_URL" | cut -d ' ' -f 1);
      if [[ $ARCHIVE_LOCAL_MD5 == $ARCHIVE_REMOTE_MD5 ]]; then
        >&2 echo "archive md5 match $ARCHIVE_LOCAL_URL"
        return 0;
      else
        >&2 echo "archive md5 incorrect $ARCHIVE_LOCAL_URL"
        return 1;
      fi
    else
      >&2 echo "missing archive $ARCHIVE_LOCAL_URL"
      return 1;
    fi
}

download_archive() {
    local ARCHIVE_REMOTE_URL="$1";
    local ARCHIVE_LOCAL_URL="$2";
    local ARCHIVE_REMOTE_MD5="$3";

    >&2 echo "downloading $ARCHIVE_REMOTE_URL";
    curl -L "$ARCHIVE_REMOTE_URL" > "$ARCHIVE_LOCAL_URL";

    local RESULT=$(check_archive "$ARCHIVE_REMOTE_URL" "$ARCHIVE_LOCAL_URL" "$ARCHIVE_REMOTE_MD5");
    if [[ $RESULT -eq 0 ]]; then
      >&2 echo "successfully downloaded $ARCHIVE_LOCAL_URL";
    else
      >&2 echo "downloaded archive is corrupt $ARCHIVE_LOCAL_URL";
    fi
    return $RESULT;
}

# download and verify bcl2fastq source code archive
if [[ -f "$BCL2FASTQ_ARCHIVE_LOCAL" ]]; then
  local RESULT=$(check_archive $BCL2FASTQ_ARCHIVE_URL $BCL2FASTQ_ARCHIVE_LOCAL $BCL2FASTQ_ARCHIVE_URL_MD5);
  if [[ $RESULT -ne 0 ]]; then
    exit 1
  fi
else
  local RESULT=$(download_archive $BCL2FASTQ_ARCHIVE_URL $BCL2FASTQ_ARCHIVE_LOCAL $BCL2FASTQ_ARCHIVE_URL_MD5);
  if [[ $RESULT -ne 0 ]]; then
    exit 1
  fi
fi

# download and verify boost patch
if [[ -f "$BCL2FASTQ_BOOST_PATCH_LOCAL" ]]; then
  local RESULT=$(check_archive $BCL2FASTQ_BOOST_PATCH_URL $BCL2FASTQ_BOOST_PATCH_LOCAL $BCL2FASTQ_BOOST_PATCH_MD5);
  if [[ $RESULT -ne 0 ]]; then
    exit 1
  fi
else
  local RESULT=$(download_archive $BCL2FASTQ_BOOST_PATCH_URL $BCL2FASTQ_BOOST_PATCH_LOCAL $BCL2FASTQ_BOOST_PATCH_MD5);
  if [[ $RESULT -ne 0 ]]; then
    exit 1
  fi
fi

# extract source code and apply patch
if [[ ! -d "$BCL2FASTQ_SOURCE" ]]; then
    >&2 echo "extracting source code from archive $BCL2FASTQ_ARCHIVE_LOCAL";
    ( cd "$BCL2FASTQ_WORK_DIRECTORY";
      unzip -p "$BCL2FASTQ_ARCHIVE_LOCAL" | tar -xvzf - 
      ( cd "$BCL2FASTQ_SOURCE"
        ( cd src/cxx/lib/io;
          >&2 echo "applying boost patch";
          patch < "$BCL2FASTQ_BOOST_PATCH_LOCAL";
        )
      )
    )
fi

# create build directory
if [[ ! -d "$BCL2FASTQ_BUILD" ]]; then
    >&2 echo "creating build directory $BCL2FASTQ_BUILD";
    mkdir -p "$BCL2FASTQ_BUILD";
fi

( cd "$BCL2FASTQ_BUILD";

  >&2 echo "configuring bcl2fastq";
  $BCL2FASTQ_SOURCE/src/configure

  >&2 echo "making bcl2fastq";
  make;

  >&2 echo "installing bcl2fastq";
  make install;
)