656 lines
20 KiB
Bash
Executable File
656 lines
20 KiB
Bash
Executable File
#!/usr/bin/env bash
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# Copyright 2024 Bryan C. Roessler
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#
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# This is a code scratchpad for organizing the Hartman Lab Server workflow
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# It contains a mixture of code/pseudocode and shouldn't be run until this message is removed
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#
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# Allow indirect functions
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# shellcheck disable=SC2317
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#
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# shdoc info
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# @name HartmanLabWorkflow
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# @brief One script to rule them all (see: xkcd #927)
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# @description Executes the Hartman Lab image analysis workflow
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# @option -p<value> | --project=<value> Include one or more projects in the analysis
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# @option -i<value> | --include=<value> Include one or more modules in the analysis (default: all modules)
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# @option -x<value> | --exclude=<value> Exclude one or more modules in the analysis
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# @option -y | --yes | --auto Assume yes answer to all questions (non-interactive mode)
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# @option -d | --debug Turn on extra debugging output
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# @option -h | --help Print help message and exit (overrides other options)
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DEBUG=1 # Turn debugging ON by default during development
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shopt -s extglob
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# @section Libraries
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# @description Change these variables to use different libraries
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JAVA="${JAVA:-java}"
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PYTHON="${PYTHON:-python3}"
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PERL="${PERL:-perl}"
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# @section Help
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# @description Print a helpful message
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print_help() {
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debug "Running: ${FUNCNAME[0]}"
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install_dependencies --get-depends # Loads the dependency arrays
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cat <<-EOF
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USAGE:
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script-run-workflow [[OPTION] [VALUE]]...
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Some options (--project, --include, --exclude) can be passed multiple times or
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by using comma deliminated strings (see EXAMPLES below)
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OPTIONS:
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--project, -p PROJECT
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PROJECT should follow the pattern ${PROJECT_PREFIX}_PROJECT_NAME
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--include, -i MODULE
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See MODULES section below for list of available modules
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If no --include is specified, all modules are run
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--exclude, -x MODULE
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See MODULES section below for list of modules to exclude
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--yes, -y, --auto
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Always answer yes to questions (non-interactive mode)
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--debug, -d
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Print extra debugging info
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--help, -h
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Print this help message and exit
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MODULES:
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${ALL_MODULES[*]}
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SUBMODULES:
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${ALL_SUBMODULES[*]}
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DEPENDENCIES:
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deb: ${depends_deb[@]}
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rpm: ${depends_rpm[@]}
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brew: ${depends_brew[@]}
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perl: ${depends_perl[@]}
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R: ${depends_r[@]}
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BiocManager: ${depends_bioc[@]}
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EXAMPLES:
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script-run-workflow --module ${ALL_MODULES[0]} --module ${ALL_MODULES[1]}
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script-run-workflow --project ${PROJECT_PREFIX}_MY_PROJECT --module ${ALL_MODULES[0]} --module ${ALL_MODULES[1]}
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script-run-workflow --project ${PROJECT_PREFIX}_MY_PROJECT --module ${ALL_MODULES[1]} --module ${ALL_MODULES[2]} --yes
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script-run-workflow --module=${ALL_MODULES[0]},${ALL_MODULES[1]}
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script-run-workflow --project=${PROJECT_PREFIX}_MY_PROJECT,${PROJECT_PREFIX}_MY_OTHER_PROJECT
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script-run-workflow --project=${PROJECT_PREFIX}_MY_PROJECT,${PROJECT_PREFIX}_MY_OTHER_PROJECT --module=${ALL_MODULES[1]},${ALL_MODULES[2]} --yes --debug
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EOF
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}
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# @section User Input
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# @description Creates array and switches from user input
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parse_input() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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long_opts="project:,include:,exclude:,yes,auto,debug,help"
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short_opts="+p:i:x:yhd"
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if input=$(getopt -o $short_opts -l $long_opts -- "$@"); then
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eval set -- "$input"
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while true; do
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case $1 in
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--project|-p)
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shift
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if [[ $1 == *','* ]] ; then # check for commas
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IFS=',' read -ra PROJECTS <<< "$1"
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else
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PROJECTS+=("$1")
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fi
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;;
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--include|-i)
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shift
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if [[ $1 == *','* ]] ; then # check for commas
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IFS=',' read -ra INCLUDE_MODULES <<< "$1"
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else
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INCLUDE_MODULES+=("$1")
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fi
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;;
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--exclude|-x)
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shift
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if [[ $1 == *','* ]] ; then # check for commas
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IFS=',' read -ra EXCLUDE_MODULES <<< "$1"
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else
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EXCLUDE_MODULES+=("$1")
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fi
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;;
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--yes|-y|--auto)
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declare -g YES=1
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;;
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--debug|-d)
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declare -g DEBUG=1
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;;
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--help|-h)
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print_help; exit 0
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;;
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--)
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shift
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break
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;;
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esac
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shift
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done
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else
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err "Incorrect options provided"; exit 1
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fi
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}
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# @section Helper functions
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# @internal
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module() {
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debug "Adding $1 module"
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ALL_MODULES+=("$1")
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declare -gA "$1"
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}
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submodule() {
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debug "Adding $1 submodule"
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ALL_SUBMODULES+=("$1")
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declare -gA "$1"
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}
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# This function will only work if users have an actual name registered on the server
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# TODO for now just use username
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# user_initials() {
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# user_record="$(getent passwd "$(whoami)")"
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# user_gecos_field="$(echo "$user_record" | cut -d ':' -f 5)"
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# user_full_name="$(echo "$user_gecos_field" | cut -d ',' -f 1)"
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# last="${user_full_name#* }"
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# echo "${user_full_name:0:1}${last:0:1}"
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# }
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ask() {
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declare response
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(( YES )) && return 0
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read -r -p "$* [y/N]: " response
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[[ ${response,,} =~ ^(yes|y)$ ]]
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}
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err() { echo "Error: $*" >&2; }
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ask_pn() {
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declare -g PROJECT
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read -r -p "Enter a full project name (ex. ${PROJECT_PREFIX}_PROJECT_NAME): " PROJECT
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}
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debug() { (( DEBUG )) && echo "Debug: $*"; }
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# @section Modules
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# @description A module contains a cohesive set of actions/experiments to run on a project
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# Use a module when:
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# * Building a new type of analysis
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# * Combining submodules
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#
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#
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module install_dependencies
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# @description Installs dependencies for the workflow
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install_dependencies() {
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debug "Running: ${FUNCNAME[0]}" "$@"
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# Dependency arrays
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depends_rpm=(graphviz pandoc pdftk-java gd-devel shdoc)
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depends_deb=(graphviz pandoc pdftk-java libgd-dev shdoc)
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depends_brew=(graphiz pandoc gd pdftk-java shdoc)
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depends_perl=(File::Map ExtUtils::PkgConfig GD GO::TermFinder)
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depends_r=(BiocManager ontologyIndex ggrepel tidyverse sos openxlsx ggplot2
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plyr extrafont gridExtra gplots stringr plotly ggthemes pandoc rmarkdown)
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depends_bioc=(org.Sc.sgd.db)
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[[ $1 == "--get-depends" ]] && return 0 # if we just want to read the depends vars
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# Install system-wide dependencies
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echo "Installing system dependencies"
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case "$(uname -s)" in
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Linux*|CYGWIN*|MINGW*)
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ask "Detected Linux platform, continue?" || return 1
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echo "You may be prompted for your sudo password to install system packages"
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if hash dnf &>/dev/null; then
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sudo dnf install "${depends_rpm[@]}"
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elif hash apt &>/dev/null; then
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sudo apt install "${depends_deb[@]}"
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fi
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;;
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Darwin*)
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ask "Detected Mac platform, continue?" || return 1
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export HOMEBREW_BREW_GIT_REMOTE="https://github.com/Homebrew/brew"
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curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh|bash
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brew install "${depends_brew[@]}"
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;;
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*)
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echo "Your system could not be detected, please install dependencies manually"
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;;
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esac
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# Install perl CPAN modules
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echo "Installing perl CPAN modules"
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debug "cpan" "${depends_perl[@]}"
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cpan "${depends_perl[@]}"
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# Install R packages
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echo "Installing R packages"
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depends_r_str=""
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depends_r_to_string() {
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for d in "${depends_r[@]}"; do
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depends_r_str+="$d\", \""
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done
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depends_r_str="${depends_r_str::-3}" # strip last , " (comma and quote)
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}
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depends_r_to_string
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debug "Rscript -e install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
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Rscript -e "install.packages(c(\"$depends_r_str), dep=TRUE, repos=\"https://cloud.r-project.org\")"
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Rscript -e "BiocManager::install(\"${depends_bioc[0]}\")"
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}
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module init_job
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# @section Initialize a new job in the scans directory
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# @description Create a new ExpJobs project
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# TODO Copy over source image directories from robot - are these alse named by the ExpJobs name?
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init_job() {
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debug "Running: ${FUNCNAME[0]}"
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if [[ -d $SCAN_DIR ]]; then
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ask "$SCAN_DIR already exists, re-initialize?" || return 0
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else
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ask "Initialize a new project at $SCAN_DIR?" || return 1
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mkdir -p "$SCAN_DIR"
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fi
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[[ -d $SCAN_DIR/MasterPlateFiles ]] || mkdir -p "$SCAN_DIR/MasterPlateFiles"
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DRUG_MEDIA_FILE="$SCAN_DIR/MasterPlateFiles/DrugMedia_$PROJECT.xls"
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MASTER_PLATE_FILE="$SCAN_DIR/MasterPlateFiles/MasterPlate_$PROJECT.xls"
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# TODO Where are the actual templates?
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for f in $DRUG_MEDIA_FILE $MASTER_PLATE_FILE; do
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touch "$f"
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done
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}
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module easy
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# @section EASY
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# @description Start an EASY analysis
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# The QHTCPImageFolders and ‘MasterPlateFiles’ folder are the inputs for image analysis with EASY software.
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# EASY will automatically generate a ‘Results’ directory (within the ExpJobs/‘ExperimentJob’ folder) w/ timestamp and an optional short description provided by the user (Fig.2).
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# The ‘Results’ directory is created and entered, using the “File >> New Experiment” dropdown in EASY.
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# Multiple ‘Results’ files may be created (and uniquely named) within an ‘ExperimentJob’ folder.
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easy() {
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debug "Running: ${FUNCNAME[0]}"
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EASY="/mnt/data/EASY/EasyDev2024/BU/EASY240430AppExported/EstartConsole.m"
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pushd "$SCAN_DIR" || return 1
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# Launch graphical matlab if the user wants
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ask "Start EASY in MATLAB? This requires a GUI." && matlab -nosplash -r "$EASY"
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# glob EASY output and make sure it exists
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shopt -s nullglob
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EASY_RESULTS_DIRS=( Results* )
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shopt -u nullglob
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[[ ${#EASY_RESULTS_DIRS} -ge 1 ]] || (echo "Missing EASY output"; exit 1)
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declare -a EASY_OUT_ARRAY
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for EASY_RESULTS_DIR in "${EASY_RESULTS_DIRS[@]}"; do
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[[ -d $EASY_RESULTS_DIR ]] && echo "Found EASY Results directory: $EASY_RESULTS_DIR"
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EASY_PRINT_RESULTS_DIR="$EASY_RESULTS_DIR/PrintResults"
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[[ -d $EASY_PRINT_RESULTS_DIR ]] && echo "Found EASY PrintResults directory: $EASY_PRINT_RESULTS_DIR"
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EASY_PRINT_RESULTS_FILES=(
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"$EASY_PRINT_RESULTS_DIR/!!"*
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"$EASY_PRINT_RESULTS_DIR"/NoGrowth_*.txt
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"$EASY_PRINT_RESULTS_DIR"/GrowthOnly_*.txt
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)
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EASY_OUT_ARRAY+=("$EASY_RESULTS_DIR" "$EASY_PRINT_RESULTS_DIR" "${EASY_PRINT_RESULTS_FILES[@]}")
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done
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echo "EASY OUTPUT ARRAY: " "${EASY_OUT_ARRAY[@]}"
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}
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module ezview
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# @section EZView
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ezview() {
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debug "Running: ${FUNCNAME[0]}"
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EZVIEW_DIR="/mnt/data/EZVIEW"
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echo "$EZVIEW_DIR"
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}
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module qhtcp
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# @section QHTCP
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# @description Main QHTCP module (functional rewrite of REMcMaster3.sh)
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qhtcp() {
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debug "Running: ${FUNCNAME[0]}"
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TEMPLATE_DIR="$SCRIPT_DIR/templates/qhtcp"
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QHTCP_DIR="/mnt/data/StudiesQHTCP/$PROJECT"
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# Our list of submodules (functions) to run for this module
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# Put these in the appropriate order of operations
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submodules=(
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r_join_interact
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java_extract
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r_add_shift_values
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r_heat_maps_zscores
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r_heat_maps_homology
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py_gtf
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r_compile_gtf
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)
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while [[ -d $QHTCP_DIR ]]; do
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echo "A project already exists at $QHTCP_DIR"
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ask "Safely update $QHTCP_DIR from the $TEMPLATE_DIR template?" && break
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if ask "Back up $QHTCP_DIR to $QHTCP_DIR.bk and start fresh?"; then
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mv "$QHTCP_DIR" "$QHTCP_DIR.bk" || (echo "Backup unsuccessful, exiting"; exit 1)
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fi
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done
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# Copy template to QHTCP project directory
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if rsync --archive --update "$TEMPLATE_DIR"/ "$QHTCP_DIR"; then
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echo "New project created at $QHTCP_DIR"
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fi
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# Create StudyInfo.csv
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# Right now this is identical to the template but we can change it later
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cat <<-EOF > "$QHTCP_DIR/Code/StudyInfo.csv"
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ExpNumb,ExpLabel,BackgroundSD,ZscoreJoinSD,AnalysisBy
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1,ExpName1,NA,NA,UserInitials
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2,ExpName2,NA,NA,UserInitials
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3,ExpName3,NA,NA,UserInitials
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4,ExpName4,NA,NA,UserInitials
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EOF
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# Enter REMc directory to run the scripts there
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pushd "$QHTCP_DIR/REMc" || return 1
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# Run each submodule
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for s in "${submodules[@]}"; do "$s"; done
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popd || return 1
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}
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# @section Submodules
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# @description Submodules provide functionaility to modules and are reusable between modules
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# Use a submodule when:
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# * Calling external scripts
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# * Performing repetitive tasks
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# *
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#
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submodule r_join_interact
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# @description JoinInteractExps3dev.R creates REMcRdy_lm_only.csv and Shift_only.csv
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r_join_interact() {
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debug "Running: ${FUNCNAME[0]}"
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echo "Rscript JoinInteractExps3dev.R"
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Rscript JoinInteractExps3dev.R
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out_file="REMcRdy_lm_only.csv"
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out_file2="Shift_only.csv"
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for f in "$out_file" "$out_file2"; do
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[[ -f $f ]] || (echo "$f does not exist"; return 1)
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done
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}
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submodule java_extract
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# @description Jingyu's REMc java utility using file input file REMcRdy_lm_only.csv
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# and output REMcRdy_lm_only.csv-finalTable.csv
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java_extract() {
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debug "Running: ${FUNCNAME[0]}"
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classpath="jingyuJava_1_7_extractLib.jar"
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out_file="REMcRdy_lm_only.csv-finalTable.csv"
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# backup REMcRdy_lm_only.csv-finalTable.csv
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[[ -f $out_file ]] && mv "$out_file" "$out_file.bk"
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java_cmd=(
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"$JAVA" -Xms512m -Xmx2048m -Dfile.encoding=UTF-8 -classpath "$classpath" ExecMain
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"REMcRdy_lm_only.csv"
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"GeneByGOAttributeMatrix_nofiltering-2009Dec07.tab"
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"ORF_List_Without_DAmPs.txt" 1 true true
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)
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echo "${java_cmd[@]}"
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"${java_cmd[@]}"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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}
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submodule r_add_shift_values
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# @description Add shift values back to REMcRdy_lm_only.csv-finalTable.csv
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# and output "REMcWithShift.csv" for use with the REMc heat maps
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r_add_shift_values() {
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debug "Running: ${FUNCNAME[0]}"
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out_file="REMcHeatmaps/REMcWithShift.csv"
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echo "Rscript AddShiftVals2.R"
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Rscript AddShiftVals2.R
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rm -f "REMcHeatmaps/"*.pdf
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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}
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submodule r_heat_maps_zscores
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# @description Execute REMcHeatmaps_zscores.R
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r_heat_maps_zscores() {
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debug "Running: ${FUNCNAME[0]}"
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out_file="REMcHeatmaps/compiledREMcHeatmaps.pdf"
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echo "Rscript REMcHeatmaps_zscores.R"
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Rscript REMcHeatmaps_zscores.R
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pdfs=(REMcHeatmaps/*.pdf)
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echo "pdftk ${pdfs[*]} output $out_file"
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pdftk "${pdfs[@]}" output "$out_file"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
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}
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submodule r_heat_maps_homology
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# @description Execute REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R
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r_heat_maps_homology() {
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debug "Running: ${FUNCNAME[0]}"
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work_dir="REMcHeatmapsWithHomology"
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source_file="REMcHeatmaps/REMcWithShift.csv"
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target_file="$work_dir/REMcWithShift.csv"
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out_file="$work_dir/Homology/compiledREMcHomologyHeatmaps.pdf"
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echo "rsync --archive $source_file $target_file"
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rsync --archive "$source_file" "$target_file"
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# Clean old output
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rm "$work_dir/Homology/"*.{pdf,csv}
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pushd "$work_dir" || return 1
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Rscript \
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REMcHeatmaps_Z_lm_wDAmPs_andHomology_221212.R \
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REMcWithShift.csv \
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Homology \
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17_0503_DAmPs_Only.txt \
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Yeast_Human_Homology_Mapping_biomaRt_18_0920.csv
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popd || return 1
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pdfs=("$work_dir"/Homology/*.pdf)
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pdftk "${pdfs[@]}" output "$out_file"
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[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
|
||
}
|
||
|
||
|
||
submodule py_gtf
|
||
# @description Perform GTF
|
||
py_gtf() {
|
||
debug "Running: ${FUNCNAME[0]}"
|
||
process_dir="GTF/Process"
|
||
function_dir="GTF/Function"
|
||
component_dir="GTF/Component"
|
||
in_file="REMcRdy_lm_only.csv-finalTable.csv"
|
||
out_file="$process_dir/REMcRdy_lm_only/1-0-0-finaltable.csv"
|
||
echo "$PYTHON DconJG2.py $in_file $process_dir/"
|
||
"$PYTHON" DconJG2.py "$in_file" "$process_dir/"
|
||
[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
|
||
unset out_file
|
||
rsync -a "$process_dir/REMcRdy_lm_only" GTF/Function/
|
||
rsync -a "$process_dir/REMcRdy_lm_only" GTF/Component/
|
||
|
||
# @description Not sure what to name this
|
||
# @arg $1 string directory name
|
||
_process() {
|
||
debug "Running: ${FUNCNAME[0]}" "$@"
|
||
pushd "$1" || return 1
|
||
|
||
shopt -s nullglob
|
||
set2=(REMcRdy_lm_only/*.txt)
|
||
shopt -u nullglob
|
||
|
||
for s in "${set2[@]}"; do
|
||
pl_analyze "$set1" "$s"
|
||
pl_terms2tsv "$s"
|
||
"$PERL" terms2tsv_v4.pl "$s.terms" > "$s.tsv"
|
||
done
|
||
|
||
# Concat the process ontology outputs from the /REMcReady_lm_only folder
|
||
echo "$PYTHON Concatenate_GTF_results.py REMcRdy_lm_only/ $out_file"
|
||
echo "TODO: Concatenate_GTF_results.py should be translated to bash"
|
||
"$PYTHON" Concatenate_GTF_results.py REMcRdy_lm_only/ "$out_file"
|
||
|
||
[[ -f $out_file ]] || (echo "$out_file does not exist"; return 1)
|
||
popd || return 1
|
||
}
|
||
|
||
# Perform operations in each directory
|
||
for d in "$process_dir" "$function_dir" "$component_dir"; do
|
||
set1="ORF_List_Without_DAmPs.txt"
|
||
out_file="${d##*/}Results.txt" # Use the dirname to create each Results filename
|
||
_process "$d" & # parallelize
|
||
done
|
||
}
|
||
|
||
|
||
submodule pl_analyze
|
||
# @description Perl analyze submodule
|
||
# This seems weird to me because we're just overwriting the same data for all set2 members
|
||
# https://metacpan.org/dist/GO-TermFinder/view/examples/analyze.pl
|
||
# Is there a reason you need a custom version and not the original from cpan?
|
||
# @arg $1 string Set 1
|
||
# @arg $2 string Set 2
|
||
pl_analyze() {
|
||
script="analyze_v2.pl"
|
||
an="gene_association.sgd"
|
||
out_file="gene_ontology_edit.obo"
|
||
debug "$PERL $script -an $an -as P -o $out_file -b $1 $2"
|
||
"$PERL" "$script" -an "$an" -as P -o "$out_file" -b "$1" "$2"
|
||
}
|
||
|
||
|
||
submodule pl_terms2tsv
|
||
# @description Perl terms2tsv submodule
|
||
# Probably should be translated to shell/python
|
||
# @arg $1 string Set 2
|
||
pl_terms2tsv() {
|
||
script="terms2tsv_v4.pl"
|
||
debug "$PERL $script $1.terms > $1.tsv"
|
||
"$PERL" "$script" "$1.terms" > "$1.tsv"
|
||
}
|
||
|
||
|
||
submodule documentation
|
||
# @section Documentation
|
||
# @description Generates markdown documentation from this script using shdoc
|
||
documentation() {
|
||
debug "Running: ${FUNCNAME[0]}"
|
||
|
||
# Print markdown to stdout
|
||
shdoc < "$SCRIPT"
|
||
|
||
# Create markdown file
|
||
shdoc < "$SCRIPT" > documentation.md
|
||
|
||
}
|
||
|
||
|
||
|
||
|
||
# @description Compile GTF in R
|
||
r_compile_gtf() {
|
||
debug "Running: ${FUNCNAME[0]}"
|
||
echo "Rscript CompileGTF.R"
|
||
Rscript CompileGTF.R
|
||
}
|
||
|
||
|
||
# @description The main loop of script-run-workflow
|
||
# May eventually need to add git ops
|
||
# Passes on arguments
|
||
# Most variables in main() are user configurable or can be overriden by env
|
||
main() {
|
||
debug "Running: ${FUNCNAME[0]}" "$@"
|
||
|
||
# Where are we located?
|
||
SCRIPT=$(realpath -s "${BASH_SOURCE[0]}")
|
||
SCRIPT_DIR=$(dirname "$SCRIPT")
|
||
|
||
# Set the automatic project directory prefix
|
||
PROJECT_PREFIX="$(whoami)_$(date +%y_%m_%d)"
|
||
san() { [[ $1 =~ .+_[0-9][0-9]_[0-9][0-9]_[0-9][0-9]_.+ ]]; } # sanitizer regex for prefix
|
||
|
||
declare -ag PROJECTS=() # this array will hold all of the projects for this run
|
||
|
||
parse_input "$@" # parse arguments with getopt
|
||
|
||
# Prompt user for the PROJECT if we still don't have one
|
||
if [[ ${#PROJECTS[@]} -eq 0 ]]; then # still allows for environment overrides
|
||
ask_pn
|
||
PROJECTS+=("$PROJECT")
|
||
fi
|
||
|
||
for i in "${!PROJECTS[@]}"; do
|
||
if ! san "${PROJECTS[i]}"; then
|
||
echo "Project name ${PROJECTS[i]} is invalid"
|
||
echo "Enter a replacement"
|
||
ask_pn
|
||
san "$PROJECT" || (echo "RTFM"; return 1)
|
||
PROJECTS[i]="$PROJECT"
|
||
fi
|
||
done
|
||
|
||
SCANS_DIR="${SCANS_DIR:-"/mnt/data/ExpJobs"}" # TODO propose changing this to something else
|
||
|
||
# If we don't catch with getopt or env, run all
|
||
if [[ ${#INCLUDE_MODULES[@]} -eq 0 ]]; then
|
||
MODULES=("${ALL_MODULES[@]}")
|
||
else
|
||
MODULES=("${INCLUDE_MODULES[@]}")
|
||
fi
|
||
|
||
# Exclude modules from --exclude
|
||
arr=()
|
||
for m in "${MODULES[@]}"; do
|
||
[[ " ${EXCLUDE_MODULES[*]} " =~ [[:space:]]${m}[[:space:]] ]] || arr+=("$m")
|
||
done
|
||
MODULES=("${arr[@]}")
|
||
unset arr
|
||
|
||
# Sanitize MODULES
|
||
for i in "${!MODULES[@]}"; do
|
||
if ! [[ " ${ALL_MODULES[*]} " =~ [[:space:]]${MODULES[i]}[[:space:]] ]]; then
|
||
echo "Module $m not in the module list"
|
||
echo "Available modules: ${ALL_MODULES[*]}"
|
||
read -r -p "Enter replacement module name: " MODULE
|
||
! [[ " ${ALL_MODULES[*]} " =~ [[:space:]]${MODULE}[[:space:]] ]] || (echo "RTFM"; return 1)
|
||
MODULES[i]="$MODULE"
|
||
fi
|
||
done
|
||
|
||
# Loop over projects
|
||
for PROJECT in "${PROJECTS[@]}"; do
|
||
SCAN_DIR="$SCANS_DIR/$PROJECT"
|
||
|
||
# Run selected modules
|
||
for m in "${MODULES[@]}"; do
|
||
ask "Run $m" && "$m"
|
||
done
|
||
done
|
||
|
||
}
|
||
|
||
main "$@"
|
||
|
||
exit $?
|