In pvrqualitasag/qgert: Qualitas Genetic Evaluation Routine Tools

Bash Settings

```{bash, eval=FALSE} set -o errexit # exit immediately, if single command exits with non-zero status set -o nounset # treat unset variables as errors set -o pipefail # return value of pipeline is value of last command to exit with non-zero status # hence pipe fails if one command in pipe fails

## Global Constants
### prog paths
```{bash, eval=FALSE}
ECHO=/bin/echo                             # PATH to echo                            #
DATE=/bin/date                             # PATH to date                            #
BASENAME=/usr/bin/basename                 # PATH to basename function               #
DIRNAME=/usr/bin/dirname                   # PATH to dirname function                #

Directories

``{bash, eval=FALSE} INSTALLDIR=$DIRNAME ${BASH_SOURCE[0]}` # installation dir of bashtools on host #

### Files
```{bash, eval=FALSE}
SCRIPT=`$BASENAME ${BASH_SOURCE[0]}`       # Set Script Name variable                #

Hostname

``{bash, eval=FALSE} SERVER=hostname` # put hostname of server in variable #

## Function definitions local to this script
usage message
```{bash, eval=FALSE}
usage () {
  local l_MSG=$1
  $ECHO "Usage Error: $l_MSG"
  $ECHO "Usage: $SCRIPT -s <source_path_script> -t <installation_target_path>"
  $ECHO "  where -s <source_path_script>        --  source path for script"
  $ECHO "        -t <installation_target_path>  --  target path where script will be installed"
  $ECHO ""
  exit 1
}

produce a start message ``{bash, eval=FALSE} start_msg () { $ECHO "********************************************************************************" $ECHO "Starting $SCRIPT at: "$DATE +"%Y-%m-%d %H:%M:%S"` $ECHO "Server: $SERVER" $ECHO }

produce an end message
```{bash, eval=FALSE}
end_msg () {
  $ECHO
  $ECHO "End of $SCRIPT at: "`$DATE +"%Y-%m-%d %H:%M:%S"`
  $ECHO "********************************************************************************"
}

functions related to logging ``{bash, eval=FALSE} log_msg () { local l_CALLER=$1 local l_MSG=$2 local l_RIGHTNOW=$DATE +"%Y%m%d%H%M%S"` $ECHO "[${l_RIGHTNOW} -- ${l_CALLER}] $l_MSG" }

## Main part of the script starts here ...
```{bash, eval=FALSE}
start_msg

Use getopts for commandline argument parsing If an option should be followed by an argument, it should be followed by a ":". Notice there is no ":" after "h". The leading ":" suppresses error messages from getopts. This is required to get my unrecognized option code to work. ```{bash, eval=FALSE} SRCPATH="" TRGPATH="" while getopts ":s:t:h" FLAG; do case $FLAG in h) usage "Help message for $SCRIPT" ;; s) if test -f $OPTARG; then SRCPATH=$OPTARG else usage "$OPTARG isn't a regular file" fi ;; t) if [ -d "$OPTARG" ] then TRGPATH=$OPTARG else usage "$OPTARG is not an installation target directory" fi ;; :) usage "-$OPTARG requires an argument" ;; ?) usage "Invalid command line argument (-$OPTARG) found" ;; esac done

shift $((OPTIND-1)) #This tells getopts to move on to the next argument.

Check whether required arguments have been defined
```{bash, eval=FALSE}
if [ "$SRCPATH" == "" ]
then
  usage "-s <source_path> cannot be undefined"
fi

if [ "$TRGPATH" == "" ]
then
  usage "-t <target_path> cannot be undefined"
fi

log_msg $SCRIPT "Copy script from $SRCPATH to target: $TRGPATH ..."
cp $SRCPATH $TRGPATH

Script ends here ```{bash, eval=FALSE} end_msg

## Latest Update 
```{bash, latest-update, eval=TRUE} 
date 

pvrqualitasag/qgert documentation built on June 29, 2021, 11:14 p.m.