setup.sh

#!/bin/bash

JBROWSE_BUILD_MIN=${JBROWSE_BUILD_MIN:=1}
# check the exit status of the command, and print the last bit of the log if it fails
done_message() {
  if [ $? == 0 ]; then
    log_echo " done."
    if [ "x$1" != "x" ]; then
      echo $1
    fi
  else
    echo " failed.  See setup.log file for error messages." $2
    if [[ "x$3" != "x" ]]; then
      echo "setup cannot continue, aborting."
      tail -200 setup.log
      return 1
    fi
  fi
}

# echoes both to the console, and to setup.log
# adds extra carriage returns in setup.log for readability.
log_echo() {
  echo $@
  echo >>setup.log
  echo $@ >>setup.log
  echo >>setup.log
}

check_node() {
  set +e
  node_executable=$(which node)
  npm_executable=$(which npm)
  if ! [ -x "$node_executable" ]; then
    nodejs_executable=$(which nodejs)
    if ! [ -x "$nodejs_executable" ]; then
      echo "No 'node' executable found. JBrowse expects node version 6 or later. Please install an updated version of node.js by following the instructions appropriate for your system https://nodejs.org/en/download/package-manager/"
      return 1
    else
      echo "Creating an alias 'node' for 'nodejs'"
      node_executable="$nodejs_executable"
    fi
  fi
  set -e
  if ! [ -x "$npm_executable" ]; then
    echo "No 'npm' executable found. JBrowse expects npm version 3 or later. Please install an updated version of node.js by following the instructions appropriate for your system https://nodejs.org/en/download/package-manager/"
    return 1
  fi
  NODE_VERSION=$($node_executable -v)
  NODE_MAJOR_VERSION=$($node_executable -v | cut -dv -f2 | cut -d. -f1)
  NODE_MINOR_VERSION=$($node_executable -v | cut -d. -f1)
  NPM_VERSION=$($npm_executable -v)
  NPM_MAJOR_VERSION=$($npm_executable -v | cut -d. -f1)
  if [[ $NODE_MAJOR_VERSION -lt 6 ]]; then
    echo "node $NODE_VERSION found, but node version 6 or later must be installed.  Please install an updated version of node.js by following the instructions appropriate for your system https://nodejs.org/en/download/package-manager/"
    return 1
  fi
  if [[ $NPM_MAJOR_VERSION -lt 3 ]]; then
    echo "npm $NPM_VERSION found, but npm version 3 or later must be installed.  Please install an updated version of node.js by following the instructions appropriate for your system https://nodejs.org/en/download/package-manager/"
    return 1
  fi
  echo "Node $NODE_VERSION installed at $node_executable with npm $NPM_VERSION"
}

# npm 7+ keeps an existing yarn.lock "up to date" by rewriting it in npm's own
# dialect, whose multi-hash integrity lines yarn 1 cannot parse. setup.sh used to
# run a bare `npm install yarn` here, corrupting the lockfile in place, so repair
# clones that already ran it (issue #1675). yarn never emits a space inside an
# integrity value, so that space is an unambiguous signature of the rewrite.
repair_yarn_lock() {
  if grep -qE '^  integrity .+ .+' yarn.lock; then
    log_echo "yarn.lock has been rewritten by npm into a form yarn cannot parse; restoring it (issue #1675)."
    git checkout -- yarn.lock || true
    if grep -qE '^  integrity .+ .+' yarn.lock; then
      echo "ERROR: could not restore a usable yarn.lock. Restore it from a clean copy of JBrowse and run setup.sh again."
      return 1
    fi
    log_echo "Restored yarn.lock."
  fi
}

# we are starting a new setup. clear the log file
rm -f setup.log

#flag to skip everything after webpack
FAST=0
while getopts f option; do
  case "${option}" in
  f) FAST=1 ;;
  esac
done

if [ $FAST == 1 ]; then
  log_echo "Fast build requested."
fi

# log information about this system
log_echo -n "Gathering system information ..."
(
  echo '============== System information ===='
  set -x
  lsb_release -a
  uname -a
  sw_vers
  grep MemTotal /proc/meminfo
  echo
  echo
) >>setup.log 2>&1
done_message "" ""

# check Mac OS version
SUPPRESS_BIODB_TO_JSON=0

sw_vers >&/dev/null
if [ $? -eq 0 ]; then
  product_version=$(sw_vers -productVersion)
  have_db=$(perl -MConfig=myconfig -e 'print myconfig' | grep -- -ldb)
  if [[ $product_version =~ ^10.13 && x$have_db = 'x' ]]; then
    SUPPRESS_BIODB_TO_JSON=1
    log_echo
    log_echo ===============================================================
    log_echo "** MacOS High Sierra with broken system Perl detected. **"
    log_echo "biodb-to-json.pl does not work on MacOS High Sierra with the stock system Perl."
    log_echo "The setup will not run biodb-to-json.pl for its sample data: Volvox and Yeast."
    log_echo "To re-enable formatting on your High Sierra machine, install a Perl with a working BerkeleyDB."
    log_echo
    log_echo "If you use Homebrew, an easy way to install a working Perl would be:"
    log_echo
    log_echo "    brew install berkeley-db; brew install --build-from-source perl"
    log_echo
    log_echo "Then delete the external perl libraries and run setup.sh again:"
    log_echo
    log_echo "    rm -rf extlibs/; ./setup.sh"
    log_echo
    log_echo ===============================================================
    log_echo
  fi
fi

log_echo "NOTE: Legacy scripts wig-to-json.pl and bam-to-json.pl have been removed from setup. Their functionality has been superseded by add-bam-track.pl and add-bw-track.pl. If you require the old versions, please use JBrowse 1.12.3 or earlier."

# if we are running in a development build, then run npm install and run the webpack build.
if [ -f "src/JBrowse/Browser.js" ]; then
  log_echo -n "Installing node.js dependencies and building with webpack ..."
  (
    set -e
    check_node
    repair_yarn_lock
    # --no-save --no-package-lock: keep npm from rewriting yarn.lock into its
    # own dialect, which yarn 1 cannot parse
    [[ -f node_modules/.bin/yarn ]] || npm install --no-save --no-package-lock yarn
    node_modules/.bin/yarn install
    JBROWSE_BUILD_MIN=$JBROWSE_BUILD_MIN node_modules/.bin/yarn build
  ) >>setup.log 2>&1
  done_message "" "" "FAILURE NOT ALLOWED"
else
  log_echo "Minimal release, skipping node and Webpack build (note: this version will not allow using plugins. Use a github clone or a dev version of JBrowse to use plugins"
fi

if [ $FAST == 1 ]; then
  log_echo "Fast build requested; skipping installing Perl prerequisites and sample data. Exiting..."
  exit 0
fi

log_echo -n "Installing Perl prerequisites ..."
if ! (perl -MExtUtils::MakeMaker -e 1 >/dev/null 2>&1); then
  log_echo
  log_echo "WARNING: Your Perl installation does not seem to include a complete set of core modules.  Attempting to cope with this, but if installation fails please make sure that at least ExtUtils::MakeMaker is installed.  For most users, the best way to do this is to use your system's package manager: apt, yum, fink, homebrew, or similar."
fi
(
  set -x
  bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 </dev/null
  bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 </dev/null
  set -e
  bin/cpanm -v --notest -l extlib/ Bio::Perl@1.7.2 </dev/null
  set -x
  bin/cpanm -v --notest -l extlib/ --installdeps . </dev/null
  bin/cpanm -v --notest -l extlib/ --installdeps . </dev/null
  set -e
  bin/cpanm -v --notest -l extlib/ --installdeps . </dev/null
) >>setup.log 2>&1
done_message "" "As a first troubleshooting step, make sure development libraries and header files for GD, Zlib, and libpng are installed and try again."

log_echo
log_echo -n "Formatting Volvox example data ..."
(
  set -e
  set -x

  # format volvox
  rm -rf sample_data/json/volvox
  bin/prepare-refseqs.pl --fasta docs/tutorial/data_files/volvox.fa --out sample_data/json/volvox
  if [ $SUPPRESS_BIODB_TO_JSON -eq 1 ]; then
    echo "Not running biodb-to-json.pl for Volvox"
  else
    bin/biodb-to-json.pl -v --conf docs/tutorial/conf_files/volvox.json --out sample_data/json/volvox
  fi

  cat \
    docs/tutorial/data_files/volvox_microarray.bw.conf \
    docs/tutorial/data_files/volvox_sine.bw.conf \
    docs/tutorial/data_files/volvox-sorted.bam.conf \
    docs/tutorial/data_files/volvox-sorted-nomd.bam.conf \
    docs/tutorial/data_files/volvox-samspec.bam.conf \
    docs/tutorial/data_files/volvox-sorted.bam.coverage.conf \
    docs/tutorial/data_files/volvox-paired.bam.conf \
    docs/tutorial/data_files/volvox.vcf.conf \
    docs/tutorial/data_files/volvox_fromconfig.conf \
    docs/tutorial/data_files/volvox.gff3.conf \
    docs/tutorial/data_files/volvox.gtf.conf \
    docs/tutorial/data_files/volvox.sort.gff3.gz.conf \
    docs/tutorial/data_files/volvox.sort.gff3.gz.htmlfeatures.conf \
    docs/tutorial/data_files/volvox.sort.bed.gz.conf \
    docs/tutorial/data_files/gvcf.vcf.gz.conf \
    docs/tutorial/data_files/bookmarks.conf \
    docs/tutorial/data_files/volvox.subsubparts.gff3.conf \
    docs/tutorial/data_files/volvox-long-reads.fastq.sorted.bam.conf \
    docs/tutorial/data_files/volvox-long-reads.fastq.sorted.cram.conf \
    docs/tutorial/data_files/volvox.bb.conf \
    docs/tutorial/data_files/volvox-sorted.cram.conf \
    docs/tutorial/data_files/volvox-sv.bam.conf \
    docs/tutorial/data_files/volvox-sv.cram.conf \
    docs/tutorial/data_files/volvox-bed12.bed.gz.conf \
    >>sample_data/json/volvox/tracks.conf

  bin/add-json.pl '{ "dataset_id": "volvox", "include": [ "../../raw/volvox/functions.conf" ] }' sample_data/json/volvox/trackList.json
  bin/add-json.pl '{ "dataset_id": "volvox", "plugins": [ "HideTrackLabels", "NeatCanvasFeatures", "NeatHTMLFeatures" ] }' sample_data/json/volvox/trackList.json
  bin/flatfile-to-json.pl --bed docs/tutorial/data_files/volvox_segment.bed --out sample_data/json/volvox --trackLabel ChromHMM --trackType CanvasFeatures --clientConfig '{"color": "{chromHMM}", "strandArrow": false}' --config '{"displayMode": "collapsed", "enableCollapsedMouseover": true, "category": "Miscellaneous" }'
  bin/generate-names.pl --safeMode -v --out sample_data/json/volvox

  mkdir -p sample_data/raw
  if [ ! -e sample_data/raw/volvox ]; then
    ln -s ../../docs/tutorial/data_files sample_data/raw/volvox
  fi
  ln -sf ../../docs/tutorial/conf_files/volvox.json sample_data/raw/

  touch sample_data/json/volvox/successfully_run

) >>setup.log 2>&1
done_message "To see the volvox example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/volvox."

log_echo
log_echo -n "Formatting Yeast example data ..."
(
  set -e
  set -x

  # format volvox
  rm -rf sample_data/json/yeast/
  bin/prepare-refseqs.pl --fasta sample_data/raw/yeast_scaffolds/chr1.fa.gz --fasta sample_data/raw/yeast_scaffolds/chr2.fa.gzip --out sample_data/json/yeast/
  gunzip -c sample_data/raw/yeast_scaffolds/chr1.fa.gz sample_data/raw/yeast_scaffolds/chr2.fa.gzip >sample_data/raw/yeast_chr1+2/yeast.fa
  if [ $SUPPRESS_BIODB_TO_JSON -eq 1 ]; then
    echo "Not running biodb-to-json.pl for Yeast"
  else
    bin/biodb-to-json.pl --conf sample_data/raw/yeast.json --out sample_data/json/yeast/
  fi
  bin/add-json.pl '{ "dataset_id": "yeast" }' sample_data/json/yeast/trackList.json
  bin/add-json.pl '{ "dataset_id": "yeast",  "plugins": [ "NeatHTMLFeatures","NeatCanvasFeatures","HideTrackLabels" ] }' sample_data/json/yeast/trackList.json
  bin/generate-names.pl --dir sample_data/json/yeast/
) >>setup.log 2>&1
done_message "To see the yeast example data, browse to http://your.jbrowse.root/index.html?data=sample_data/json/yeast."