9.2 Download and Compile PEcAn

Set R_LIBS_USER

# point R to personal lib folder
echo 'export R_LIBS_USER=${HOME}/R/library' >> ~/.profile
source ~/.profile
mkdir -p ${R_LIBS_USER}

9.2.1 Download, compile and install PEcAn from GitHub

# download pecan
cd
git clone https://github.com/PecanProject/pecan.git

# compile pecan
cd pecan
make

For more information on the capabilities of the PEcAn Makefile, check out our section on Updating PEcAn.

Following will run a small script to setup some hooks to prevent people from using the pecan demo user account to check in any code.

# prevent pecan user from checking in code
./scripts/create-hooks.sh

9.2.2 PEcAn Testrun

Do the run, this assumes you have installed the BETY database, sites tar file and SIPNET.

# create folder
cd
mkdir testrun.pecan
cd testrun.pecan

# copy example of pecan workflow and configuration file
cp ../pecan/tests/pecan32.sipnet.xml pecan.xml
cp ../pecan/scripts/workflow.R workflow.R

# exectute workflow
rm -rf pecan
./workflow.R pecan.xml

NB: pecan.xml is configured for the virtual machine, you will need to change the field from ‘/home/carya/’ to wherever you installed your ‘sites’, usually $HOME