Phylonium on HPC

David Jorgensen

2020/05/01

Build from git

Phylonium needs to be compiled from the github repository. As we do not have sudo rights on the cluster, this requires a mix of conda and installed modules. Once GCC in Anaconda is updated to 8.2.0 this should no longer be necessary. The following should be run line-by-line in the shell, answering yes to dependencies and installs.

module load anaconda3/personal

conda create -n phylonium_build
source activate phylonium-build

conda install gsl automake git gxx_linux-64

#this lib is the reason we need to use conda
conda install -c bioconda libdivsufsort

#need to export the most recent gcc version installed on the cluster
export CC=/apps/gcc/8.2.0/bin/gcc

#clone the github repo and build
git clone https://github.com/evolbioinf/phylonium

#this makes a new subdir you need to work from
cd phylonium
autoreconf -fi -Im4
./configure
make

source deactivate phylonium-build

After this build is complete you should have an executable 'phylonium' in /phylonium/src/ which can be run outside of this conda environment

Format of sequences

The program requires each sequence used to be in a separate fasta file. This could be carried out with awk in bash more efficiently but I have used the following R code.

require(ape)

# IMPORTANT: set wd where you want - about to spam 10k+ sequence files!!

seqs <- read.FASTA("./your_input_multifasta.fas")

# cant have / or | in filenames
labs <- gsub("\\/", "_",gsub("\\|", "_", labels(seqs)))
names(seqs) <- labs

# progress bar for loop
pb = txtProgressBar(min = 0, max = length(seqs), initial = 0, style=3) 

for(i in 1:length(seqs)){
write.FASTA(seqs[i], paste0(names(seqs)[i], ".fas"))
  setTxtProgressBar(pb,i)
}

Shell script for qsub

As phylonium is installed locally you will need to copy the directory to $TEMPDIR on the compute node to use the command. This script copies and runs on all .fas files in the current directory. Something similar to the following should be saved as a .sh or .pbs shell script.

#PBS -S /bin/bash
#PBS -N matrix
#PBS -l select=1:ncpus=4:mem=5gb,walltime=01:00:00
#PBS -j oe

cp $PBS_O_WORKDIR/*.fas $TMPDIR
cp $HOME/phylonium/ -r $TMPDIR

./phylonium/src/phylonium *.fas > distmat.out

cp distmat.out $PBS_O_WORKDIR