#!/bin/bash

set -e

# Usage: [PYTHON=path/to/python] [DEENURP=path/to/deenurp] bootstrap.sh
#
# Create a virtualenv, and install requirements to it.
#
# specify a python interpreter using
# `PYTHON=path/to/python bootstrap.sh`
# specify path to the deenurp source directory using
# `DEENURP=path/to/deenurp bootstrap.sh`

# installs deenurp and dependencies to $VIRTUAL_ENV if defined;
# otherwise creates a virtualenv locally.

# Will attempt to install python packages from wheels if $PIP_FIND_LINKS is defined
# and pip --use-wheel is specified

# set $PIP_WHEEL_DIR and $PIP_FIND_LINKS in the parent environment if
# desired

# Will attempt to create wheels if $PIP_WHEEL_DIR is defined
# see https://pip.pypa.io/en/latest/user_guide.html#environment-variables


mkdir -p src
SRCDIR=$(readlink -f src)

if [[ -n "$PIP_WHEEL_DIR" ]]; then
    mkdir -p "$PIP_WHEEL_DIR"
fi

srcdir(){
    tar -tf $1 | head -1
}

if [[ -n "$1" ]]; then
    venv="$1"
elif [[ -n $VIRTUAL_ENV ]]; then
    venv=$VIRTUAL_ENV
else
    venv=$(basename $(pwd))-env
fi

if [[ -z $PYTHON ]]; then
    PYTHON=$(which python2)
fi

# Defines the default source directory for deenurp as the parent of
# the directory containing this file.
if [[ -z $DEENURP ]]; then
    DEENURP=$(cd $(dirname $BASH_SOURCE) && cd .. && pwd)
fi

VENV_VERSION=15.1.0
PPLACER_BUILD=1.1.alpha19
INFERNAL_VERSION=1.1.2
RAXML_VERSION=8.0.5
MUSCLE_VERSION=3.8.31
VSEARCH_VERSION=2.6.2

check_version(){
    # usage: check_version module version-string
    "$PYTHON" <<EOF 2> /dev/null
import $1
from distutils.version import LooseVersion
assert LooseVersion($1.__version__) >= LooseVersion("$2")
EOF
}

# create virtualenv if necessary, downloading source if available
# version is not up to date.
VENV_URL="https://github.com/pypa/virtualenv/archive/${VENV_VERSION}"
if [[ ! -f "${venv:?}/bin/activate" ]]; then
    # if the system virtualenv is up to date, use it
    if check_version virtualenv $VENV_VERSION; then
      echo "using $(which virtualenv) (version $(virtualenv --version))"
	    virtualenv "$venv"
    else
	echo "downloading virtualenv version $VENV_VERSION"
	if [[ ! -f src/virtualenv-${VENV_VERSION}/virtualenv.py ]]; then
	    mkdir -p src
	    (cd src && \
		wget --quiet -nc ${VENV_URL}.tar.gz && \
		tar -xf ${VENV_VERSION}.tar.gz)
	fi
	"$PYTHON" src/virtualenv-${VENV_VERSION}/virtualenv.py "$venv"
    fi
else
    echo "virtualenv $venv already exists"
fi

source $venv/bin/activate

# full path; set by activate
venv=$VIRTUAL_ENV

# Preserve the order of installation. The requirements are sorted so
# that secondary (and higher-order) dependencies appear first. See
# bin/pipdeptree2requirements.py. We use --no-deps to prevent various
# packages from being repeatedly installed, uninstalled, reinstalled,
# etc. Also, enfoprcing the order of installation ensures that
# install-time dependencies are met (`pip install -r requirements.txt`
# fails due to a install-time dependency that cogent has for numpy)
pip2 install -U pip

# install pysqlite and updated sqlite3 libraries
wget --quiet -O - \
     https://raw.githubusercontent.com/fhcrc/taxtastic/master/dev/install_pysqlite.sh | bash

while read pkg; do
    pip2 install "$pkg" --no-deps --upgrade
done < <(/bin/grep -v -E '^#|^$' "$DEENURP/requirements.txt")

pip2 install "$DEENURP"

# install pplacer and accompanying python scripts
PPLACER_DIR=pplacer-Linux-v${PPLACER_BUILD}
PPLACER_ZIP=${PPLACER_DIR}.zip

pplacer_is_installed(){
    $venv/bin/pplacer --version 2> /dev/null | grep -q "$PPLACER_BUILD"
}

if pplacer_is_installed; then
    echo -n "pplacer is already installed: "
    $venv/bin/pplacer --version
else
    mkdir -p src && \
	(cd src && \
	wget -nc --quiet https://github.com/matsen/pplacer/releases/download/v$PPLACER_BUILD/$PPLACER_ZIP && \
	unzip -o $PPLACER_ZIP && \
	cp $PPLACER_DIR/{pplacer,guppy,rppr} $venv/bin && \
	pip2 install -U $PPLACER_DIR/scripts)
    # confirm that we have installed the requested build
    if ! pplacer_is_installed; then
	echo -n "Error: you requested pplacer build $PPLACER_BUILD "
	echo "but $($venv/bin/pplacer --version) was installed."
	echo "Try removing src/$PPLACER_ZIP first."
	exit 1
    fi
fi

# install infernal and easel binaries
INFERNAL=infernal-${INFERNAL_VERSION}-linux-intel-gcc

if [ ! -f $venv/bin/cmalign ]; then
    (cd src && \
	wget -nc --quiet http://eddylab.org/infernal/${INFERNAL}.tar.gz && \
	for binary in cmalign cmconvert cmcalibrate cmsearch esl-alimerge esl-sfetch; do
	    tar xvf ${INFERNAL}.tar.gz --no-anchored binaries/$binary
	done && \
	    cp ${INFERNAL}/binaries/* $venv/bin && \
	    rm -r ${INFERNAL}
    )
else
    echo "cmalign is already installed: $(cmalign -h | sed -n 2p)"
fi

# install FastTree and FastTreeMP
if [ ! -f $venv/bin/FastTree ] | [ ! -f $venv/bin/FastTreeMP ]; then
    (cd $venv/bin && \
	wget -nc --quiet http://www.microbesonline.org/fasttree/FastTree && \
	wget -nc --quiet http://www.microbesonline.org/fasttree/FastTreeMP && \
	chmod +x FastTree*)
else
    echo "FastTree is already installed: $(FastTree -expert 2>&1 | head -1)"
fi

# install raxmlHPC-SSE3 and raxmlHPC-PTHREADS-SSE3
if [ ! -f $venv/bin/raxmlHPC-SSE3 ] | [ ! -f $venv/bin/raxmlHPC-PTHREADS-SSE3 ]; then
    (cd src && \
	wget -nc --quiet https://github.com/stamatak/standard-RAxML/archive/v${RAXML_VERSION}.tar.gz && \
	tar -xf v${RAXML_VERSION}.tar.gz && \
	cd standard-RAxML-${RAXML_VERSION} && \
	rm -f *.o && make --jobs 4 --file Makefile.SSE3.gcc && \
	rm -f *.o && make --jobs 4 --file Makefile.SSE3.PTHREADS.gcc && \
	mv raxmlHPC-SSE3 raxmlHPC-PTHREADS-SSE3 $venv/bin
    )
else
    echo "raxml is already installed: $(raxmlHPC-SSE3 | grep RAxML)"
fi

echo $venv

# install VSEARCH
vsearch_is_installed(){
    $venv/bin/vsearch --version | grep -q "$VSEARCH_VERSION"
}

if vsearch_is_installed; then
    echo -n "vsearch is already installed: "
    $venv/bin/vsearch --version
else
    echo "installing vsearch"
    (cd src && \
	    wget -nc --quiet https://github.com/torognes/vsearch/releases/download/v${VSEARCH_VERSION}/vsearch-${VSEARCH_VERSION}-linux-x86_64.tar.gz && \
	    tar -xf vsearch-${VSEARCH_VERSION}-linux-x86_64.tar.gz && \
	    cp vsearch-${VSEARCH_VERSION}-linux-x86_64/bin/vsearch $venv/bin && \
	    chmod +x $venv/bin/vsearch
    )
fi

# install MUSCLE
muscle_is_installed(){
    $venv/bin/muscle -version | grep -q "$MUSCLE_VERSION"
}

if muscle_is_installed; then
    echo -n "muscle is already installed: "
    $venv/bin/muscle -version
else
    echo "installing muscle"
    (cd src && \
	    wget -nc --quiet http://www.drive5.com/muscle/downloads${MUSCLE_VERSION}/muscle${MUSCLE_VERSION}_src.tar.gz && \
	    tar -xf muscle${MUSCLE_VERSION}_src.tar.gz && \
	    cd muscle${MUSCLE_VERSION}/src && \
	    ./mk && cp muscle $venv/bin)
fi