Source

DunnHowisonZapata2013 / 08b-phylogeny.sh

#!/bin/sh
#SBATCH -t 96:00:00
#SBATCH -c 16
#SBATCH --mem=60g
#SBATCH -C e5-2600

export BIOLITE_RESOURCES="database=$PWD/biolite.sqlite,agalma_database=$PWD/agalma.sqlite,outdir=$PWD/analyses,threads=16,memory=60g"

set -e

cd scratch

ID=AgalmaExampleTree

agalma treeprune --id $ID
agalma multalign --id $ID --supermatrix
agalma genetree --id $ID --raxml_flags="-o Hydra_magnipapillata,Nematostella_vectensis" --bootstrap 0