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DunnHowisonZapata2013 / 08-phylogeny.sh

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#!/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

module load agalma/0.3.3

ID=AgalmaExampleTree
LOAD_IDS=`diagnostics list -n load 2>/dev/null | awk 'NR>1 {print $2}'`

agalma homologize --id $ID --load_ids $LOAD_IDS
agalma multalign --id $ID
agalma genetree --id $ID
agalma treeprune --id $ID
agalma multalign --id $ID --supermatrix
agalma genetree --id $ID --raxml_flags="-o Hydra_magnipapillata,Nematostella_vectensis"