#!/usr/bin/env bash

# Install script for BPM, based off BCE.

# To provision a new BPM VM, get the latest BCE. Boot it, then open a terminal
# and do: 
#
#    cd /usr/local/bin
#    sudo wget https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/bpm-bce/bpm-update-2015-spring
#    sudo chmod +x bpm-update-2015-spring
#    sudo bpm-update-2015-spring bpm-public
#
# This creates a VM that can be exported and shared without restriction. Additional
# license-restricted packages can be installed for internal sharing with:
#
#    sudo bpm-update bpm-ucbling
#
# Note that the bpm-public target symlinks bpm-update-VERSION to bpm-update, and the
# shorter form can be used thereafter.
#
# Individual packages can be installed or updated with:
#
#    sudo bpm-update <package>
#
# To list available packages:
#
#    bpm-update --help

# Also ran this on host so that symlinks can be created in shared folder:
# VBoxManage setextradata BCE-0.1.3dev VBoxInternal2/SharedFoldersEnableSymlinksCreate/bpm-bce-mods 1
# from template:
# VBoxManage setextradata <VM_NAME> VBoxInternal2/SharedFoldersEnableSymlinksCreate/<SHARE_NAME> 1

VERSION=BCE-2015-spring-BPM-2-public
VERSION_SUFFIX=`echo $VERSION | cut -f 2,3 -d-`   # e.g. 2015-spring
SCRIPTDIR=/usr/local/bin
BARE_SCRIPTNAME=bpm-update
VERSIONED_SCRIPTNAME="$BARE_SCRIPTNAME-$VERSION_SUFFIX"
ABS_BARE_SCRIPTNAME="$SCRIPTDIR/$BARE_SCRIPTNAME"
ABS_VERSIONED_SCRIPTNAME="$SCRIPTDIR/$VERSIONED_SCRIPTNAME"

APT_GET="apt-get -q -y"
ORIGDIR=`pwd`

# Make heredoc variable assignment pretty.
define(){ read -r -d '' ${1} || true; }

# Install/remove .deb packages with apt-get.
# First argument is install|remove
# Second argument is a newline-delimited list of packages (# comment lines allowed).
# Third argument is message to echo to console.
apt_get_packages(){
    echo "${3}"
    # The grep bit allows us to have comments in the packages file
    # The quotation marks around ${1} preserves newlines.
    $APT_GET ${1} $(grep '^[^#]' <(echo "${2}")) && \
    $APT_GET clean && \ # help avoid running out of disk space
    echo DONE: ${3} || echo FAIL: ${3}
}

# Package installs will fail if we are not up to date.
apt_get_update(){
    $APT_GET update
}

# Install the version.txt file on the desktop.
install_version_txt() {
    echo "Installing version.txt to the desktop."
    echo "Installed version will be $VERSION. Press 'y' to confirm."
    read -n 1 confirm
    if [ "$confirm" != 'y' ]; then
        echo "Edit bpm-update to update VERSION. Exiting."
        exit 1
    fi
    cat > /home/oski/Desktop/version.txt << EOF
$VERSION
EOF
    echo "Installed version.txt."
}

# Create a symlink from bpm-update-VERSION to bpm-update.
symlink_bpm-update() {
    echo "Creating symlink to $ABS_BARE_SCRIPTNAME from $ABS_VERSIONED_SCRIPTNAME."
    ln -s $ABS_VERSIONED_SCRIPTNAME $ABS_BARE_SCRIPTNAME && \
    echo "DONE: Created symlink." || { echo "FAIL: Could not create symlink. Is $VERSIONED_SCRIPTNAME in $SCRIPTDIR? Or are you trying to run "; exit 1; }
}

# Self-update the bpm-update script.
# Adapted from http://stackoverflow.com/questions/8595751/is-this-a-valid-self-update-approach-for-a-bash-script
update_bpm-update() {
    echo "Updating bpm_update"

    UPDATE_BASE=https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/bpm-bce

    # Download new version
    if ! wget --quiet --output-document="$ABS_VERSIONED_SCRIPTNAME".tmp $UPDATE_BASE/$VERSIONED_SCRIPTNAME ; then
        echo "Failed: Error while trying to wget new version!"
        echo "File requested: $UPDATE_BASE/$VERSIONED_SCRIPTNAME"
        exit 1
    fi

    # Copy over modes from old version
    OCTAL_MODE=$(stat -c '%a' $ABS_VERSIONED_SCRIPTNAME)
    if ! chmod $OCTAL_MODE "$ABS_VERSIONED_SCRIPTNAME.tmp" ; then
        echo "Failed: Error while trying to set mode on $ABS_VERSIONED_SCRIPTNAME.tmp."
        exit 1
    fi

    # Create and spawn update script
    cat > overwrite_bpm-update.sh << EOF
#!/bin/bash

# Overwrite old file with new
if mv "$ABS_VERSIONED_SCRIPTNAME.tmp" "$ABS_VERSIONED_SCRIPTNAME"; then
  echo 'Done. Update of "$ABS_VERSIONED_SCRIPTNAME" complete.'
else
  echo 'Failed to update "$ABS_VERSIONED_SCRIPTNAME"!'
fi
# Remove overwrite_bpm-update.sh and return to specified directory.
rm \$0
cd "\$1"
EOF

    echo -n "Inserting update process..."
    exec /bin/bash overwrite_bpm-update.sh "$ORIGDIR"
}

# Clone and set up python package from github.
# First argument is base github url.
# Second argument is specific repo (package) on github.
python_clone_and_setup(){
    cd /usr/local/src
    git clone ${1}/${2}
    cd ${2}
    python setup.py install
    cd ..
    rm -rf ${2}
    cd $ORIGDIR
}

add_bpm_repositories(){
    # Add neurodebian and sil.org repositories.
    msg="BPM-BCE: Adding Linguistics repositories..."
    echo "$msg"
    # neurodebian
    wget -O- http://neuro.debian.net/lists/trusty.us-ca.full | \
    tee /etc/apt/sources.list.d/neurodebian.sources.list && \
    apt-key adv --recv-keys --keyserver hkp://pgp.mit.edu:80 2649A5A9 && \
    # sil.org
    echo "deb http://packages.sil.org/ubuntu utopic main" > /etc/apt/sources.list.d/sil.sources.list && \
    wget http://packages.sil.org/sil.gpg -O- | apt-key add - && \
    # ppa for ffmpeg--should no longer be necessary, starting with Ubuntu 15.04
    add-apt-repository ppa:kirillshkrogalev/ffmpeg-next && \   # Ubuntu 14.10
    #add-apt-repository ppa:mc3man/trusty-media && \   # Ubuntu 14.04
    echo DONE: $msg || echo FAIL: $msg
}

fix_sil(){
    # Fix problem with sil repo pointing to wrong ubuntu version.
    echo "deb http://packages.sil.org/ubuntu utopic main" > /etc/apt/sources.list.d/sil.sources.list
}

fix_audio_rate(){
    # Fix issue with modprobe not identifying correct rate for ac97 sound device.
    msg="Fixing audio rate."
    echo $msg
    FIX_CNT=$(grep 'options snd-intel8x0 ac97_clock=48000' /etc/modprobe.d/alsa-base.conf|wc -l)
    if [ "$FIX_CNT" == "0" ]
    then
        echo '# Fix audio rate issue where ac97 clock not correctly identified.' >> /etc/modprobe.d/alsa-base.conf
        echo 'options snd-intel8x0 ac97_clock=48000' >> /etc/modprobe.d/alsa-base.conf
        echo 'Audio fix applied. Reboot the virtual machine to finish.'
    else
        echo 'Audio fix already applied. No changes have been made.'
    fi
}

fix_pyalign(){
    # Fix problem with align.py found after VERSION=BCE-2015-spring-BPM-1-public.
    FNAME=align.py
    msg="Fixing align.py."
    echo $msg
    cd /opt/p2fa && \
    cp $FNAME $FNAME.orig && \
    wget --quiet --output-document="$FNAME" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/p2fa/$FNAME && \
    chmod +x $FNAME && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

fix_klsyn(){
    # Fix problem with klsyn found after VERSION=BCE-2015-spring-BPM-2-public.
    pip install xlrd
    pip install xlwt
}

ling113_get_dict(){
    # Get a script to download dict.local for Ling113, spring 2015.
    FNAME=ling113_get_local_dict
    msg="Getting ling113_get_dict"
    echo $msg
    cd /usr/local/bin && \
    wget --quiet --output-document="$FNAME" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/bash/$FNAME && \
    chmod +x $FNAME && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

ling290_vot(){
    # The VOT script used in Ling290, Fall 2015.
    FNAME=VOT_290.py
    msg="Getting VOT_290.py"
    echo $msg
    cd /usr/local/bin && \
    wget --quiet --output-document="$FNAME" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/python/$FNAME && \
    chmod +x $FNAME && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_ecog(){
    FNAME1=ecog_ucsf.py
    FNAME2=htkmfc.py
    msg="Getting ecog_ucsf.py and htkmfc.py"
    echo $msg
    cd /usr/local/lib/python2.7/dist-packages && \
    wget --quiet --output-document="$FNAME1" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/python/$FNAME1 && \
    wget --quiet --output-document="$FNAME2" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/python/$FNAME2 && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_bce_packages(){
    # These are packages that install from repositories already enabled in BCE.
define STDPKGS <<'EOF'
imagemagick
praat
sox
wavesurfer

# wish8.5 is needed for wavesurfer but is not installed automatically. This is
# probably a Depends bug in the wavesurfer package.
tcl8.5
tk8.5

# We need to install osspd-alsa so that praat is not removed automatically when
# pulseaudio is removed.
osspd-alsa

# The following packages are needed in order to build espsfree-* on the vm.
# They will no longer be necessary and can be removed when espsfree-*
# can be downloaded as a binary package.
#build-essential  # already in BCE
byacc
#debhelper  # already in BCE
devscripts
flex
libatlas-dev

# Needed to compile esps.
libc6-dev-i386

# Needed to compile htk (results in package authentication warnings).
libx11-dev:i386
EOF
    apt_get_packages install "$STDPKGS" "BPM-BCE: Installing Linguistics packages from standard repositories..."
    # praat playback fails when pulseaudio is installed and vm is running on an os x host
    apt_get_packages "remove --purge --assume-yes" pulseaudio "BPM-BCE: Removing pulseaudio..."
}


install_neuro_packages(){
    # Packages from the neurodebian repository.
define NEUROPKGS <<'EOF'
opensesame
EOF
    apt_get_packages install "$NEUROPKGS" "BPM-BCE: Installing Linguistics packages from neurodebian repository..."
    msg="Installing media_player_vlc plugin."
    echo $msg
    FNAME=media_player_vlc.zip
    PLUGDIR=/home/oski/.opensesame/plugins
    mkdir -p $PLUGDIR && \
    cd $PLUGDIR && \
    wget --quiet --output-document="$FNAME" https://github.com/rsprouse/ucblingmisc/raw/master/opensesame/$FNAME && \
    unzip $FNAME && \
    chown -R oski.oski /home/oski/.opensesame && \
    rm $FNAME && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_fieldworks(){
    # Packages from the sil.org repository.
define SILPKGS <<'EOF'
fieldworks-applications
EOF
    apt_get_packages install "$SILPKGS" "BPM-BCE: Installing Linguistics packages from sil.org repository..."
}

install_ipa(){
    # Packages from the sil.org repository.
    # See http://scripts.sil.org/cms/scripts/page.php?site_id=nrsi&id=UniIPAKeyboard#dfc8e3bf for install
    # instructions and http://linux.lsdev.sil.org/wiki/index.php/Installing_KMFL_on_Ubuntu for user instructions
    # on keyboard selection.
define SILPKGS <<'EOF'
fonts-sil-charissil
fonts-sil-doulossil
ibus-kmfl
ibus-table
ibus-table-ipa-x-sampa
kmfl-keyboard-ipa
EOF
    apt_get_packages install "$SILPKGS" "BPM-BCE: Installing IPA packages from sil.org repository..."
    msg="Adding IPA input method."
    echo $msg
    SCHEMADIR=/usr/share/glib-2.0/schemas
    FNAME=30_org.freedesktop.ibus.general.gschema.override
    cd $SCHEMADIR && \
    wget --quiet --output-document="$FNAME" https://github.com/rsprouse/ucblingmisc/raw/master/bpm-bce/resources/$FNAME && \
    glib-compile-schemas $SCHEMADIR && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_ffmpeg(){
define FFMPEGPKGS <<'EOF'
ffmpeg
EOF
    apt_get_packages install "$FFMPEGPKGS" "BPM-BCE: Installing Linguistics packages from ffmpeg repository..."
}

install_splalign(){
    # Install splalign.py
    msg="Installing splalign.py. We do not have permission to distribute this software. We will attempt to install from a local .zip file."
    echo $msg
    cd /opt/ && \
    unzip /home/oski/Desktop/splalign.zip && \
    ln -s /opt/SPLaligner/HTK_sed_for_octalCrossBasic.sh /usr/local/bin/ && \
    ln -s /opt/SPLaligner/splalign.py /usr/local/bin/ && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_phylogenetics(){
define PHYLOPKGS <<'EOF'
mrbayes
beast-mcmc
EOF
    apt_get_packages install "$PHYLOPKGS" "BPM-BCE: Installing Linguistics packages for phylogenetics..."
    msg="Installing Mesquite"
    echo $msg
    FNAME=Mesquite301_Linux.tgz
    cd /opt && \
    wget --quiet --output-document="$FNAME" https://github.com/MesquiteProject/MesquiteCore/releases/download/3.01/$FNAME && \
    tar xf $FNAME && \
    chmod +x /opt/Mesquite_Folder/mesquite.sh && \
    chown -R oski.oski /opt/Mesquite_Folder/ && \
    rm $FNAME && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_lingpy(){
    # Required by klsyn
    pip install xlrd
    pip install xlwt

    # Python packages to pull and set up from github.
    GITBASE=https://github.com/rsprouse
    python_clone_and_setup $GITBASE klsyn
    python_clone_and_setup $GITBASE audiolabel
    python_clone_and_setup $GITBASE paramdraw
    python_clone_and_setup $GITBASE maedasyn

    # Install from ucblingmisc.
    msg="Install miscellaneous Linguistics python utilities."
    echo $msg
    FNAME1=SoundLabel.pm
    FNAME2=concat_pyalign_textgrids
    FNAME3=convertlabel
    FNAME4=make_text_grids
    FNAME5=fricative_analysis.py
    FNAME6=vc_transitions
    mkdir -p /usr/local/lib/site_perl && \
    cd /usr/local/lib/site_perl && \
    wget --quiet --output-document="$FNAME1" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/perl/$FNAME1 && \
    cd /usr/local/bin && \
    wget --quiet --output-document="$FNAME2" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/perl/$FNAME2 && \
    chmod +x $FNAME2 && \
    wget --quiet --output-document="$FNAME3" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/perl/$FNAME3 && \
    chmod +x $FNAME3 && \
    wget --quiet --output-document="$FNAME4" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/perl/$FNAME4 && \
    chmod +x $FNAME4 && \
    wget --quiet --output-document="$FNAME5" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/python/$FNAME5 && \
    chmod +x $FNAME5 && \
    wget --quiet --output-document="$FNAME6" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/python/$FNAME6 && \
    chmod +x $FNAME6 && \
    echo DONE: $msg || echo FAIL: $msg

    # Install pyalign.
    msg="Install pyalign."
    echo $msg
    FNAME1=p2fa_1.003.tgz
    FNAME2=pyalign
    FNAME3=align.py
    cd /opt && \
    wget --quiet --output-document="$FNAME1" http://www.ling.upenn.edu/phonetics/p2fa/$FNAME1 && \
    tar xzvf p2fa_1.003.tgz && \
    cd /usr/local/bin && \
    wget --quiet --output-document="$FNAME2" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/python/$FNAME2 && \
    chmod +x $FNAME2 && \
    fix_pyalign && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_ultratils(){
    GITBASE=https://github.com/rsprouse
    python_clone_and_setup $GITBASE ultratils
}

install_esps(){
    # esps install
    cd /usr/local/src
    git clone https://github.com/rsprouse/espsfree
    cd espsfree/espsfree-dev
    debuild --no-tgz-check -us -uc
    cd ..
    # Use * in the .deb name so we don't have to edit this script when the version changes.
    dpkg -i espsfree-dev*.deb
    cd espsfree-lib
    debuild --no-tgz-check -us -uc
    cd ..
    dpkg -i espsfree-lib*.deb
    cd espsfree-util
    debuild --no-tgz-check -us -uc
    cd ..
    dpkg -i espsfree-util*.deb
    cd espsfree-signal
    debuild --no-tgz-check -us -uc
    cd ..
    dpkg -i espsfree-signal*.deb
    rm *.build
    rm *.changes
    rm *.deb
    rm *.dsc
    rm *.tar.gz
    rm -rf /usr/local/src/espsfree
    cd $ORIGDIR
}


install_ifcformant(){
    # Install ifcformant.
    msg="Install ifcformant."
    echo $msg
    FNAME=ifcformant-bpm-bce.tar
    cd /usr/local/src && \
    wget --quiet --output-document="$FNAME" https://github.com/rsprouse/ucblingmisc/raw/master/ifcformant-bpm/$FNAME && \
    tar xf $FNAME && \
    cd ifcformant-bpm-bce && \
    ./install-bpm.sh && \
    cd .. && \
    rm $FNAME && \
    rm -rf ifcformant-bpm-bce && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_htk(){
    # Install HTK.
    msg="Install HTK 3.4.1 for p2fa (pyalign)."
define htkprompt <<'EOF'
The HTK toolkit requires a username and password to download. These can be obtained at no cost
by registering at http://htk.eng.cam.ac.uk/register.shtml.

If you choose to skip registration HTK will not be installed. The Penn Force Aligner p2fa (pyalign)
requires HTK and will not work without it.

Provide a username to download HTK 3.4.1 or press <Enter> to skip HTK installation.
EOF
    echo $msg
    echo "$htkprompt"
    read username
    if [ $username != '' ]; then
        echo "Provide your HTK password:"
        read password
        if [ $password != '' ]; then
            FNAME=HTK-3.4.1.tar.gz
            cd /usr/local/src && \
            wget --user $username --password $password --quiet --output-document="$FNAME" http://htk.eng.cam.ac.uk/ftp/software/$FNAME && \
            tar xf $FNAME && \
            cd htk && \
            # Patch up HRec.c. See https://groups.google.com/forum/#!topic/fave-users/wDScrDkF44Q
            # and https://github.com/JoFrhwld/FAVE/wiki/HTK-on-OS-X#fixing-htk-source for details.
            perl -pi.orig -e 's/if \(dur<=0 && labid != splabid\) HError\(8522,"LatFromPaths: Align have dur<=0 "\)/if (dur<=0 && labpr != splabid) HError(8522,"LatFromPaths: Align have dur<=0 ")/' HTKLib/HRec.c && \
            ./configure && \
            # Patch up a Makefile parse error (make expects indentation with a tab character).
            perl -pi.orig -e 's/        if /\tif /' HLMTools/Makefile && \
            make all && \
            make install && \
            cd .. && \
            rm $FNAME && \
            rm -rf htk && \
            echo DONE: $msg || echo FAIL: $msg
            cd $ORIGDIR
        fi
    fi
}

# R packages for linguists.
install_r_packages(){
define r_cmd <<'EOF'
install.packages(
    c(
      "gdata",
      "languageR"
    ),
    repos = "http://cran.cnr.Berkeley.edu")
EOF
echo $r_cmd | sudo /usr/bin/Rscript --no-restore --no-save -
}

# wine depends on ttt-mscorefont-installer and requires user to accept a license agreement
install_wine(){
    # Needed for EdgeTrak
    apt_get_packages install wine "BPM-BCE: Installing wine from standard repositories..."
}

install_edgetrak(){
    # Install EdgeTrak.
    # EdgeTrak will run with:
    #   wine /opt/EdgeTrak/EdgeTrak.exe
    # Note: user must configure wine to enable 'Emulate a virtual desktop'.
    msg="Install EdgeTrak."
    echo $msg
    #FNAME=EdgeTrak.zip
    FNAME=Edgetrak.zip
    cd /opt
    #wget --quiet --output-document="$FNAME" http://speech.umaryland.edu/programs/$FNAME && \
    wget --quiet --output-document="$FNAME" https://github.com/rsprouse/ucblingmisc/raw/master/edgetrak/$FNAME && \
    unzip $FNAME && \
    rm $FNAME && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_mcr(){
    # Install Matlab MCR.
    msg="Installing Matlab runtime."
    echo $msg
    echo "This is a large download and might take a while..."
    FNAME=MCR_R2014b_glnxa64_installer.zip
    cd /usr/local/src && \
    mkdir -p matlab_installer && \
    cd matlab_installer && \
    wget --output-document="$FNAME" http://www.mathworks.com/supportfiles/downloads/R2014b/deployment_files/R2014b/installers/glnxa64/$FNAME && \
    unzip $FNAME && \
    #./install -mode silent -agreeToLicense yes -destinationFolder /opt/matlab/2014b && \
    ./install -destinationFolder /opt/matlab/2014b && \
    rm $FNAME && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

update_sources_list(){
    # Install a new sources.list with repository locations for unmaintained utopic distribution.
    msg="Installing sources.list."
    echo $msg
    FNAME=sources.list
    cd /etc/apt
    mv sources.list sources.list.old
    wget --quiet --output-document="$FNAME" https://raw.githubusercontent.com/rsprouse/ucblingmisc/master/bpm-bce/${FNAME}-2015-spring && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_display_acq(){
    # Install display_acq.
    msg="Installing display_acq."
    echo $msg
    FNAME=display_acq_2014b.tar
    cd /usr/local/bin && \
    wget --quiet --output-document="$FNAME" https://github.com/rsprouse/ucblingmisc/raw/master/display_acq-bpm/$FNAME && \
    tar xf $FNAME && \
    chmod +rx run_display_acq.sh && \
    chmod +rx display_acq && \
    rm $FNAME && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

install_creak_detect(){
    # Install creak_detect.
    msg="Installing creak_detect"
    echo $msg
    FNAME=creak_detect_web_install
    cd /usr/local/bin && \
    wget --quiet --output-document="$FNAME" https://github.com/rsprouse/ucblingmisc/raw/master/creak_detect-bpm/$FNAME && \
    chmod +rx creak_detect_web_install && \
    ./creak_detect_web_install &&\
    rm $FNAME && \
    perl -pi.orig -e 's/  MCRROOT="\$1"/  MCRROOT=\/usr\/local\/MATLAB\/MATLAB_Runtime\/v85\//' /usr/local/creak_detect/application/run_creak_detect.sh && \
    perl -pi -e 's/\\<deployedMCRroot\\> args/wavfile1 [wavfile2] [...wavfileN]/' /usr/local/creak_detect/application/run_creak_detect.sh && \
    perl -pi -e 's/echo ([S\-L"])/#echo \1/' /usr/local/creak_detect/application/run_creak_detect.sh && \
    perl -pi -e 's/shift 1/#shift 1/' /usr/local/creak_detect/application/run_creak_detect.sh && \
    #perl -pi -e 's/-gt 0/-gt 2/' /usr/local/creak_detect/application/run_creak_detect.sh && \
    perl -pi -e 's/\${exe_dir}\/creak_detect/\/usr\/local\/creak_detect\/application\/creak_detect/' /usr/local/creak_detect/application/run_creak_detect.sh && \
    ln -s /usr/local/creak_detect/application/run_creak_detect.sh /usr/local/bin/creak_detect && \
    echo DONE: $msg || echo FAIL: $msg
    cd $ORIGDIR
}

define usage <<'EOF'

  bpm-update
    Provisioning script for installing and updating Berkeley Phonetics Machine
    (BPM) packages.

  Usage:
    bpm-update <target>     # install or update package <target>
    bpm-update --help       # full usage info and list of targets

EOF

define targets <<'EOF'

Targets not installed in the BPM public release:

  fieldworks
    SIL FieldWorks packages

  htk
    HTK toolkit, required for Penn Forced Aligner p2fa (pyalign)
    (user must register at http://htk.eng.cam.ac.uk/register.shtml
    in order to download the package)

  mcr
    Matlab Component Runtime (2014b), required for display_acq
    (user must accept license agreement)

  phylogenetics
    MrBayes, BEAST, Mesquite

  wine
    Windows emulator, required for EdgeTrak
    (user must accept license agreement)

Targets that are installed in the BPM public release. Use these to reinstall
or update:

  bce-packages
    Packages that are available in the BCE package repository but not already
    installed in BCE (imagemagick, praat, sox, wavesurfer).

  display_acq
    Matlab tool for multichannel signal display, as produced in UC Berkeley
    Phonology Lab.
    (requires Matlab Component Runtime, which user can install with mcr target)

  edgetrak
    EdgeTrak tool for working with ultrasound images

  esps
    Entropic Signal Processing System (ESPS) command line utilities

  ffmpeg
    ffmpeg utility for working with video, audio, and image files

  ifcformant
    Inverse Filter Control formant tracker

  splalign
    SPLaligner, a derivative of p2fa for aligning French by Peter Milne.
    Installs from a local .zip file since UC Berkeley Phonology Lab does
    not have permission to distribute this package.

  lingpy
    Various Python packages used in the UC Berkeley Phonology Lab: audiolabel,
    klsyn, maedasyn

  neuro
    Packages from neurodebian repository: opensesame

  r-packages
    A useful set of R packages for linguists.
  
  fix-pyalign
    Fix pyalign found in VERSION=BCE-2015-spring-BPM-1-public.

  fix-klsyn
    Fix klsyn found in VERSION=BCE-2015-spring-BPM-2-public.

  fix-sil
    Fix sil repo found in VERSION=BCE-2015-spring-BPM-2-public.

  ultratils
    Install python code for processing Ultrasonix ultrasound data.

  ipa
    SIL fonts containing IPA characters and input methods (keyboard mappings).

  ling113-get-dict
    A download script for grabbing dict.local for Ling113, spring 2015.

  ling290-vot
    The VOT script for Ling290, Fall 2015.

  ecog
    Various utilities for working with ecog data.

Special purpose targets:

  bpm-update
    Use this target to self-update bpm-update.

  bpm-public
    Use this target to provision BPM additions to a BCE release.

  bpm-ucbling
    Use this target after bpm-public to provision an internal BPM release.

  apt-get
    Use this target to update the apt database before installing a target
    that includes a .deb file.

EOF

case "$1" in

# Base package installation for public release. 
bpm-public)
    symlink_bpm-update
    install_version_txt
    add_bpm_repositories
    apt_get_update
    install_bce_packages
    install_neuro_packages
    install_ffmpeg
    install_lingpy
    install_esps
    install_r_packages
    install_ifcformant
    install_edgetrak
    install_display_acq
    apt-get -q -y autoremove
    ;;

# Additional package installs for internal vm release only (license required).
bpm-ucbling)
    install_htk
    install_wine
    install_mcr
    ;;

# Self-update bpm-update.
bpm-update)
    update_bpm-update
    ;;

bce-packages)
    install_bce_packages
    ;;

# Get new sources.list for unmaintained utopic distribution.
sources-list)
    update_sources_list
    apt_get_update
    ;;

# Individual package install/update.
fix-pyalign)
    fix_pyalign
    ;;

fix-klsyn)
    fix_klsyn
    ;;

fix-sil)
    fix_sil
    ;;

fix-audio-rate)
    fix_audio_rate
    ;;

ultratils)
    install_ultratils
    ;;

neuro)
    apt_get_update
    install_neuro_packages
    ;;

ffmpeg)
    apt_get_update
    install_ffmpeg
    ;;

lingpy)
    install_lingpy
    ;;

esps)
    install_esps
    ;;

ifcformant)
    install_ifcformant
    ;;

htk)
    install_htk
    ;;

splalign)
    install_splalign
    ;;

r-packages)
    install_r_packages
    ;;

wine)
    install_wine
    ;;

edgetrak)
    install_edgetrak
    ;;

mcr)
    install_mcr
    ;;

display_acq)
    install_display_acq
    ;;

creak_detect)
    install_creak_detect
    ;;

phylogenetics)
    install_phylogenetics
    ;;

fieldworks)
    apt_get_update
    install_fieldworks
    ;;

ipa)
    apt_get_update
    install_ipa
    ;;

ling113-get-dict)
    ling113_get_dict
    ;;

ling290-vot)
    ling290_vot
    ;;

ecog)
    install_ecog
    ;;

# Miscellaneous commands that don't do any installs.
apt-get)
    apt_get_update
    ;;

--help)
    echo " "
    echo "$usage"
    echo " "
    echo "$targets"
    echo " "
    ;;

*)
    echo " "
    echo "$usage"
    echo " "
    ;;

esac

# Install voicesauce. This will require getting the source and compiling for linux.
#cd /usr/local/src
#wget http://www.phonetics.ucla.edu/voicesauce/current/VoiceSauce_bin.zip
#cd $ORIGDIR


# TODO: voicesauce, flowanalyzer