21 lines
638 B
Bash
Executable File
21 lines
638 B
Bash
Executable File
#! /bin/bash
|
|
set -e
|
|
if [ "$#" -ne 4 ]; then
|
|
echo "Usage: $0 <alignment.fa> <output_prefix> <threads> <outgroup>"
|
|
echo "Run modeltest-ng and raxml-ng on a given alignment"
|
|
exit 1
|
|
fi
|
|
|
|
aln=$(readlink -f "$1")
|
|
out=$2
|
|
threads=$3
|
|
outgroup=$4
|
|
outdir=$(dirname "$out")
|
|
mkdir -p "$outdir"
|
|
# run modeltest-ng
|
|
modeltest-ng -p "$threads" -r 12345 --force -i "$aln" -d nt -t ml -o "$out".modeltest
|
|
# run raxml-ng
|
|
cmd=$(grep "raxml-ng" "$out".modeltest.out | tail -n 1 | sed 's/> //')
|
|
params="--blopt nr_safe --all --bs-trees 1000 --outgroup $outgroup --redo --threads $threads --seed 12345 --prefix $out"
|
|
bash -c "$cmd $params" >/dev/null
|