run.generic.sh

#!/bin/bash

# Attempt to install StochKit 2.0.11
#
# Install it in the user's home folder by default, to override
#
#


#read -p "Select a directory to use as StochSS home (leave blank to use current directory): " MY_PATH

MY_PATH="`dirname \"$0\"`"              # relative
MY_PATH="`( cd \"$MY_PATH\" && pwd )`"  # absolutized and normalized
STOCHSS_HOME=$MY_PATH
STOCHSS_HOME="`( cd \"$STOCHSS_HOME\" && pwd )`" 

echo "Installing in $STOCHSS_HOME"

if [ "$(echo $STOCHSS_HOME | grep " ")" != "" ]; then
    echo "Cannot execute StochSS under any directory that contains spaces (which the filename listed above has). This is an known issue"
    exit -1
fi

function check_pyurdme {
    RET=`python -c "import pyurdme" 2>/dev/null`
    RC=$?
    if [[ $RC == 0 ]];then
        return 0 #True
    fi
    return 1 #False
}

function check_spatial_installation {
    if check_pyurdme; then
        echo "PyURDME detected successfully"
    else
        echo "PyURDME not installed, Failing (check if all required python modules are installed)."
        return 1 #False
    fi
    return 0 #True
}

#####################

function retry_command {
    if [ -z "$1" ];then
        return 1 #False
    fi

    for i in `seq 1 3`;
    do
        echo "$1"
        eval "$1"
        RET=$?
        if [[ $RET != 0 ]] ;then
            echo "Failed to execute: \"$1\""
        else
            return 0 # True
        fi
    done

    echo "Failed to execute: \"$1\", Exiting"
    exit -1
}

if check_spatial_installation;then
    echo "Spatial libraries installed correctly"
else
    echo "Error checking the spatial libraries"
    exit 1
fi

STOCHKIT_VERSION=StochKit2.0.11
STOCHKIT_PREFIX=$STOCHSS_HOME
export STOCHKIT_HOME="$STOCHKIT_PREFIX/$STOCHKIT_VERSION"
ODE_VERSION="ode-1.0.2"
export STOCHKIT_ODE="$STOCHSS_HOME/$ODE_VERSION"
STOCHOPTIM_VERSION="stochoptim-0.5-1"
export STOCHOPTIM="$STOCHSS_HOME/$STOCHOPTIM_VERSION"
export R_LIBS="$STOCHOPTIM/library"

echo -n "Testing if StochKit2 built... "

rundir=$(mktemp -d /tmp/tmp.XXXXXX)
rm -r "$rundir" >& /dev/null

if "$STOCHKIT_HOME/ssa" -m "$STOCHKIT_HOME/models/examples/dimer_decay.xml" -r 1 -t 1 -i 1 --out-dir "$rundir" >& /dev/null; then
    echo "Yes"
    echo "$STOCHKIT_VERSION found in $STOCHKIT_HOME"
else
    echo "No"

    echo "Installing in $STOCHSS_HOME/$STOCHKIT_VERSION"

    echo "Cleaning up anything already there..."
    rm -rf "$STOCHKIT_PREFIX/$STOCHKIT_VERSION"

    if [ ! -e "$STOCHKIT_PREFIX/$STOCHKIT_VERSION.tgz" ]; then
	echo "Downloading $STOCHKIT_VERSION..."
	#curl -o "$STOCHKIT_PREFIX/$STOCHKIT_VERSION.tgz" -L "http://sourceforge.net/projects/stochkit/files/StochKit2/$STOCHKIT_VERSION/$STOCHKIT_VERSION.tgz"
	curl -o "$STOCHKIT_PREFIX/$STOCHKIT_VERSION.tgz" -L "http://sourceforge.net/projects/stochkit/files/StochKit2/StochKit2.0.11/StochKit2.0.11.tgz/download"
    fi

    echo "Building StochKit"
    echo " Logging stdout in $STOCHSS_HOME/stdout.log and "
    echo " stderr in $STOCHSS_HOME/stderr.log "
    echo " * This process will take at least 5 minutes to complete. Please be patient *"
    wd=`pwd`
    cd "$STOCHKIT_PREFIX"
    retry_command "tar -xzf \"$STOCHKIT_VERSION.tgz\""
    tmpdir=$(mktemp -d /tmp/tmp.XXXXXX)
    mv "$STOCHKIT_HOME" "$tmpdir/"
    cd "$tmpdir/$STOCHKIT_VERSION"
    STOCHKIT_HOME_R=$STOCHKIT_HOME
    export STOCHKIT_HOME="$(pwd -P)"
    ./install.sh 1>"$STOCHSS_HOME/stdout.log" 2>"$STOCHSS_HOME/stderr.log"
    export STOCHKIT_HOME=$STOCHKIT_HOME_R
    cd $wd
    mv "$tmpdir/$STOCHKIT_VERSION" "$STOCHKIT_HOME"
    rm -r "$tmpdir" >& /dev/null

    rm -r "$rundir" >& /dev/null
# Test that StochKit was installed successfully by running it on a sample model
    if "$STOCHKIT_HOME/ssa" -m "$STOCHKIT_HOME/models/examples/dimer_decay.xml" -r 1 -t 1 -i 1 --out-dir "$rundir" >& /dev/null; then
	echo "Success!"
    else
	echo "Failed"
	echo "$STOCHKIT_VERSION failed to install. Consult logs above for errors, and the StochKit documentation for help on building StochKit for your platform. Rename successful build folder to $STOCHKIT_HOME"	
	exit -1
    fi
fi

echo -n "Testing if Stochoptim built... "

rm -r "$rundir" >& /dev/null

function check_if_StochOptim_Installed {
    export R_LIBS="$STOCHOPTIM/library"
    CMD="Rscript --vanilla \"$STOCHOPTIM/exec/mcem2.r\" --model \"$STOCHOPTIM/inst/extdata/birth_death_MAmodel.R\" --data \"$STOCHOPTIM/birth_death_MAdata.txt\" --steps \"\" --seed 1 --cores 1 --K.ce 1000 --K.em 100 --K.lik 10000 --K.cov 10000 --rho 0.01 --perturb 0.25 --alpha 0.25 --beta 0.25 --gamma 0.25 --k 3 --pcutoff 0.05 --qcutoff 0.005 --numIter 10 --numConverge 1 --command 'bash' >& /dev/null"
    #echo $CMD
    eval $CMD
    RET=$?
    return "$RET"
}

if check_if_StochOptim_Installed; then
    echo "Yes"
    echo "$STOCHOPTIM_VERSION found in $STOCHOPTIM"
else
    echo "No"

    echo "Installing in $STOCHSS_HOME/$STOCHOPTIM_VERSION"

    echo "Cleaning up anything already there..."
    rm -rf "$STOCHOPTIM" >& /dev/null

    echo "Building StochOptim"
    echo " Logging stdout in $STOCHSS_HOME/stdout.log and "
    echo " stderr in $STOCHSS_HOME/stderr.log "
    echo " * This process will take at least 5 minutes to complete. Please be patient *"

    retry_command "tar -xzf \"$STOCHOPTIM.tgz\""
    mkdir "$STOCHOPTIM/library"
    RET=$?
    if [[ $RET != 0 ]] ;then
        echo "Failed to: mkdir \"$STOCHOPTIM/library\", exiting"
        exit -1
    fi

    wd=`pwd`

    echo install.packages\(\"optparse\", \""$STOCHOPTIM/library"\", \"http://cran.us.r-project.org\", INSTALL_opts = \"--no-multiarch\"\) > "$STOCHOPTIM/install_packages.R"
    echo install.packages\(\""$STOCHOPTIM"\", \""$STOCHOPTIM/library"\", NULL, type = \"source\", INSTALL_opts = \"--no-multiarch\"\) >> "$STOCHOPTIM/install_packages.R"

    Rscript "$STOCHOPTIM/install_packages.R" 1> "$STOCHSS_HOME/stdout.log" 2>"$STOCHSS_HOME/stderr.log"

    export R_LIBS="$STOCHOPTIM/library"

    # Test that StochOptim was installed successfully by running it on a sample model
    if check_if_StochOptim_Installed; then
	    echo "Success!"
    else
	    echo "Failed"
	    echo "$STOCHOPTIM failed to install. Consult logs above for errors"	
	    exit -1
    fi
fi

echo -n "Testing if StochKit2 ODE built... "

rm -r "$rundir" >& /dev/null
if "$STOCHKIT_ODE/ode" -m "$STOCHKIT_HOME/models/examples/dimer_decay.xml" -t 1 -i 1 --out-dir "$rundir" >& /dev/null; then
    echo "Yes"
    echo "ode found in $STOCHKIT_ODE"
else
    echo "No"

    echo "Installing in $STOCHSS_HOME/$ODE_VERSION"

    echo "Cleaning up anything already there..."
    rm -rf "$STOCHSS_HOME/ode" >& /dev/null

    stdout="$STOCHSS_HOME/stdout.log"
    stderr="$STOCHSS_HOME/stderr.log"
    echo "Building StochKit ODE"
    echo " Logging stdout in $STOCHSS_HOME/stdout.log and "
    echo " stderr in $STOCHSS_HOME/stderr.log "
    echo " * This process should take about a minute to complete. Please be patient *"
    wd=`pwd`
    tmpdir=$(mktemp -d /tmp/tmp.XXXXXX)
    retry_command "tar -xzf \"$STOCHKIT_ODE.tgz\""
    mv "$STOCHKIT_ODE" "$tmpdir"
    cd "$tmpdir/$ODE_VERSION/cvodes"
    retry_command "tar -xzf \"cvodes-2.7.0.tar.gz\""
    cd "cvodes-2.7.0"
    ./configure --prefix="$PWD/cvodes" 1>"$stdout" 2>"$stderr"
    if [ $? != 0 ]; then
	echo "Failed"
	echo "StochKit ODE failed to install. Consult logs above for errors, and the StochKit documentation for help on building StochKit for your platform. Rename successful build folder to $STOCHKIT_ODE"
        exit -1
    fi
    make 1>"$stdout" 2>"$stderr"
    if [ $? != 0 ]; then
	echo "Failed"
	echo "StochKit ODE failed to install. Consult logs above for errors, and the StochKit documentation for help on building StochKit for your platform. Rename successful build folder to $STOCHKIT_ODE"
        exit -1
    fi
    make install 1>"$stdout" 2>"$stderr"
    if [ $? != 0 ]; then
	echo "Failed"
	echo "StochKit ODE failed to install. Consult logs above for errors, and the StochKit documentation for help on building StochKit for your platform. Rename successful build folder to $STOCHKIT_ODE"
        exit -1
    fi
    cd ../../
    STOCHKIT_ODE_R=$STOCHKIT_ODE
    export STOCHKIT_ODE="$(pwd -P)"
    make 1>"$stdout" 2>"$stderr"
    if [ $? != 0 ]; then
	echo "Failed"
	echo "StochKit ODE failed to install. Consult logs above for errors, and the StochKit documentation for help on building StochKit for your platform. Rename successful build folder to $STOCHKIT_ODE"
        exit -1
    fi
    export STOCHKIT_ODE="$STOCHKIT_ODE_R"
    cd ../
    cd $wd
    mv "$tmpdir/$ODE_VERSION" "$STOCHKIT_ODE"

# Test that StochKit was installed successfully by running it on a sample model
    if "$STOCHKIT_ODE/ode" -m "$STOCHKIT_HOME/models/examples/dimer_decay.xml" -t 1 -i 1 --out-dir "$rundir" >& /dev/null; then
	echo "Success!"
    else
	echo "Failed"
	echo "StochKit ODE failed to install. Consult logs above for errors, and the StochKit documentation for help on building StochKit for your platform. Rename successful build folder to $STOCHKIT_ODE"
	exit -1
    fi
fi

rm -r "$rundir" >& /dev/null

echo "Configuring the app to use $STOCHKIT_HOME for StochKit... "
echo "Configuring the app to use $STOCHKIT_ODE for StochKit ODE... "
echo "Configuring the app to use $STOCHOPTIM for Stochoptim... "

ln -s "$STOCHOPTIM" stochoptim >& /dev/null
ln -s "$STOCHKIT_ODE" ode >& /dev/null
ln -s "$STOCHKIT_HOME" StochKit >& /dev/null

# Write STOCHKIT_HOME to the appropriate config file
echo "$STOCHKIT_HOME" > "$STOCHSS_HOME/conf/config"
echo "$STOCHKIT_ODE" >> "$STOCHSS_HOME/conf/config"
echo -n "$STOCHOPTIM" >> "$STOCHSS_HOME/conf/config"
echo "Done!"

exec python "$STOCHSS_HOME/launchapp.py" $0