agent
7f4e888e6a
- Updated `pixi.toml` to include new R package dependencies for MCMCtree workflow. - Modified markdown file to remove unnecessary simulation data discussion. - Introduced `.lintr` configuration for linting R scripts. - Created `mcmctree.ctl` control file for MCMCtree analysis. - Developed `mcmctree_workflow.r` script to orchestrate MCMCtree analysis with model testing and ESS checks. - Added `06.snaq.jl` script for SNaQ analysis with plotting capabilities. - Implemented `07.mcmctree.sh` bash script to run MCMCtree on multiple alignments in parallel.
30 lines
879 B
Bash
Executable File
30 lines
879 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=${THREADS:-16}
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if [ "$#" -ne 4 ]; then
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echo "Usage: $0 <aln_dir> <ml_dir> <out_dir> <alignment_ext>"
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echo "Run MCMCtree on orthogroup alignments with corresponding ML trees"
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exit 1
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fi
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aln_dir=$1
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ml_dir=$2
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out_dir=$3
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ext=$4
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mkdir -p "$out_dir"
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echo -n >mcmctree.cmds
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ctlfile=$(readlink -f "$SCRIPTS/miscs/mcmctree.ctl")
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for i in "$aln_dir"/*."$ext"; do
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j=$(basename "$i" ."$ext")
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aln=$(readlink -f "$i")
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ml_tree=$(readlink -f "$ml_dir/${j}/${j}.raxml.bestTree")
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mkdir -p "${out_dir}/${j}"
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cmd="cd ${out_dir}/${j} && Rscript $SCRIPTS/miscs/mcmctree_workflow.r"
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params="-a $aln -t $ml_tree -c ${ctlfile} -p ${j}"
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echo "$cmd $params > mcmctree.log 2>&1" >>mcmctree.cmds
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done
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xargs -t -P "$THREADS" -I cmd -a mcmctree.cmds bash -c "cmd"
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echo "MCMCtree all completed."
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