example-qsub-script.sh

#!/bin/bash

# example script for running the peak-summary.R script against a slightly more complicated input file directory structure


pipeline_dir="/ifs/home/kellys04/projects/SmithLab-split2/project_notes/peak-type-plots_ChIPSeeker"
cd "$pipeline_dir"

project_parent_dir="/ifs/home/kellys04/projects/SmithLab-split2"
sub_dirs="SmithLab_CTCF SmithLab_CTCF_no_input SmithLab_H3K27AC SmithLab_H3K27ME3 SmithLab_H3K9AC"

log_dir="logs"
mkdir -p "$log_dir"

printf "%s" "$(date +"%Y-%m-%d-%H-%M-%S")" >> "start.txt"

for sub_dir in $sub_dirs; do
    printf "${sub_dir}\n\n"
    sub_dir_name="$(basename $sub_dir)"

    project_path="${project_parent_dir}/${sub_dir}"
    project_peaks_results_path="${project_path}/pipeline/peaks/results"
    sub_paths="$(ls -1 $project_peaks_results_path | xargs)"
    for sub_path in $sub_paths; do
        qsub -wd $PWD -o :${log_dir}/ -e :${log_dir}/ -j y -N "$sub_path" <<E0F
module unload r
module load r/3.3.0
set -x
find "$project_peaks_results_path" -path "*${sub_path}*" -type f -name "peaks.bed" | xargs ./peak-summary.R --id-dirname
E0F
sleep 5
    done
done

# Copy over the results
#  rsync --dry-run -vhtrP SmithLab_* results_dir/

# Aggregate Plots
#
# project_dir="/ifs/home/kellys04/projects/ChIpSeq_2017-12-31/project_notes/peak_annotation_stats"
# peak_summary_dir="${project_dir}/peaks_summaries"
#
# ls -1 "$peak_summary_dir" | while read summary_dir; do
# (
# echo "$summary_dir"
# echo "${peak_summary_dir}/${summary_dir}"
#
# upset_pdfs="$(find "${peak_summary_dir}/${summary_dir}" -name "upsetplot.pdf")"
# # echo $upset_pdfs
# anno_piechart_pdfs="$(find "${peak_summary_dir}/${summary_dir}" -name "anno-piechart.pdf")"
# peaks_coverage_pdfs="$(find "${peak_summary_dir}/${summary_dir}" -name "peaks-coverage.pdf")"
#
#
# gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=${project_dir}/${summary_dir}_upsetplot.pdf $upset_pdfs
# gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=${project_dir}/${summary_dir}_anno_piechart.pdf $anno_piechart_pdfs
# gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=${project_dir}/${summary_dir}_peaks_coverage.pdf $peaks_coverage_pdfs
# ) &
# done
#
# # FILES="$(find /path/to/dir/ -type f -name "*.pdf" | sort)"
# # gs -dBATCH -dNOPAUSE -q -sDEVICE=pdfwrite -sOutputFile=merged_output.pdf $FILES