PhyloNet3.8.0

Basic information

Tested on (Requirements)

  • Dependencies:
    • Java JDK - 1.8.0 u112

Installation

  1. Download the jar file from the official website

    cd /share/apps/phylonet/3.8.0
wget https://bioinfocs.rice.edu/sites/g/files/bxs266/f/kcfinder/files/PhyloNet_3.8.0.jar

  2. After downloading, rename the file to PhyloNet.jar:

    mv PhyloNet_3.8.0.jar PhyloNet.jar

  3. Install the corresponding module file:

Module

#%Module1.0#####################################################################
##
## module /share/apps/modules/phylonet/3.8.0
##
## /share/apps/phylonet/3.8.0 Written by Juan Pablo Ossa Zapata
##

proc ModulesHelp { } {
    puts stderr "\tphylonet/3.8.0 - sets the Environment for Phylonet \
    \n\tin the share directory /share/apps/phylonet/3.8.0 \n"
}

module-whatis "\n\n\tSets the environment for using phylonet 3.8.0\n"

# for Tcl script use only
set     topdir          /share/apps/phylonet/3.8.0
set     version         3.8.0
set     sys             linux-x86_64

conflict phylonet

module load java/jdk-1.8.0_112

prepend-path PHYLONET_DIRECTORY               $topdir

Use

module load phylonet/3.8.0

Example slurm job file:

#!/bin/sh
#SBATCH --partition=longjobs
#SBATCH --nodes=1
#SBATCH --cpus-per-task=4
#SBATCH --ntasks=1
#SBATCH --time=2:00:00
#SBATCH --job-name=testPhylonet
#SBATCH -o %x_%j.out      # File to which STDOUT will be written
#SBATCH -e %x_%j.err      # File to which STDERR will be written
#SBATCH --mail-type=ALL
#SBATCH --mail-user=jpossaz@eafit.edu.co

module load phylonet/3.8.0

export OMP_NUM_THREADS=4

srun java -jar $PHYLONET_DIRECTORY/PhyloNet.jar mynexusfile

Make sure that your nexus file is able to use all of the allocated cpu cores.

Author

  • Juan Pablo Ossa Zapata