A minimal project template directory structure that I use for my Bioinformatic projects

createproject.sh

#!/usr/bin/env bash

#A minimal project template structure that I use for my Bioinformatic projects
#MIT License (Anand Mayakonda; [email protected])

function usage() {
	echo "createproject.sh - Create a project template directory structure

Usage:         createproject.sh [option] <project_name>

<project_name> Project name should be intuitive, easy to understand, and less confusing. Required. 	
-d             Prefixes <project_name> with ISO date for clarity. Optional but recommended."
}

if [ $# -lt 1 ];then
	usage
 exit
fi

USEDATE="false"
DT=`date +%Y-%m-%d`
USR=`whoami`
PROJ=''
PROJDIR=''


while getopts 'd' OPTION; do
	case "${OPTION}" in
		d) USEDATE="true" ;;
		*) usage
			exit 1;;
	esac
done

PROJ="${@:${OPTIND}:1}"


if [[ ${USEDATE} = "true" ]]; then
	PROJDIR="${DT}_${PROJ}"
else
	PROJDIR=${PROJ}
fi

if [[ -d "${PROJDIR}" ]]; then
	echo "ERROR: Requested project directory ${PROJDIR} already exists!"
	exit 1;
fi


echo -e "Creating project directory \"${PROJDIR}\" with standardized subdirectories"
mkdir -p ${PROJDIR}

echo "Project created on ${DT} by the user: ${USR}" > ${PROJDIR}/README


mkdir -p ${PROJDIR}/00-extdata/
echo "This directory contains any external data used for analysis" > ${PROJDIR}/00-extdata/README

mkdir -p ${PROJDIR}/01-src/
echo "Any compiled codes (C/C++/GO/Rust etc) or binaries are hosted here" > ${PROJDIR}/01-src/README

mkdir -p ${PROJDIR}/02-data/
echo "Any raw/tidy data (owned by the user) used for analysis are hosted here" > ${PROJDIR}/02-data/README

mkdir -p ${PROJDIR}/03-runme/
echo "Scripts and codes (R/Python/Julia/Notebooks/Bash etc) used for actual analysis are stored and to be run from here" > ${PROJDIR}/03-runme/README
echo "Any output generated will go to 04-results" >> ${PROJDIR}/03-runme/README

mkdir -p ${PROJDIR}/04-results/
echo "All results generated by scripts in 03-runme will be stored here" > ${PROJDIR}/04-results/README

mkdir -p ${PROJDIR}/05-tmp/
echo "This is the temp directory to store intermediate results" > ${PROJDIR}/05-tmp/README
echo "Use it carefully and DO NOT DELETE unknown directories" >> ${PROJDIR}/05-tmp/README

echo -e "Done!"