24 lines
579 B
Bash
Executable File
24 lines
579 B
Bash
Executable File
#! /bin/bash
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set -e
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SCRIPTS=${SCRIPTS:-"$PROJECTHOME/99.scripts"}
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THREADS=${THREADS:-3}
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if [ "$#" -ne 3 ]; then
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echo "Usage: $0 <in_dir> <out_dir> <ext>"
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echo "Run raxml-ng on filtered orthogroup alignments"
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exit 1
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fi
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in_dir=$(readlink -f "$1")
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out_dir=$2
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ext=$3
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mkdir -p "$out_dir"
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echo -n >raxml.cmds
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for i in "$in_dir"/*."$ext"; do
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j=$(basename "$i" ."$ext")
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out_prefix="$out_dir/${j}/${j}"
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echo "$SCRIPTS/miscs/raxml.sh $i $out_prefix 4 Zju" >>raxml.cmds
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done
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xargs -t -P "$THREADS" -I cmd -a raxml.cmds bash -c "cmd"
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echo "Raxml-ng all completed."
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