pplacer

Overview

pplacer is a program to place query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.

Version 1.1.alpha19 is installed on the CSF.

Restrictions on use

There are no restrictions on accessing this software on the CSF. It is released under the GNU GPL v3.0 license and all usage must adhere to that license.

Set up procedure

We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. See the example jobscript below for how to do this. Alternatively, you may load modulefiles on the login node and let the job inherit these settings.

Load one of the following modulefiles:

module load apps/binapps/pplacer/1.1.alpha19

Running the application

Please do not run pplacer on the login node. Jobs should be submitted to the compute nodes via batch.

Serial batch job submission

Create a batch submission script (which will load the modulefile in the jobscript), for example:

#!/bin/bash --login
#$ -cwd             # Job will run from the current directory
                    # NO -V line - we load modulefiles in the jobscript

module load apps/path/to/module/n.m

# $NSLOTS will be set to 1 for a serial job. You must give the -j flag.
# By default pplacer will use two cores. So a serial job must tell it to use 1 core.
pplacer -j $NSLOTS args...

Submit the jobscript using:

qsub scriptname

where scriptname is the name of your jobscript.

Parallel batch job submission