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DunnHowisonZapata2013 / 08a-phylogeny.sh

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#!/bin/sh
#SBATCH -t 24:00:00
#SBATCH -N 8-8
#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"
export BIOLITE_HOSTLIST=`hostlist -e -s, $SLURM_NODELIST`

set -e

cd scratch

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