ngs_RSYNC.sh

#!/bin/bash

# Copyright (c) 2012,2013, Stephen Fisher and Junhyong Kim, University of
# Pennsylvania.  All Rights Reserved.
#
# You may not use this file except in compliance with the Kim Lab License
# located at
#
#     http://kim.bio.upenn.edu/software/LICENSE
#
# Unless required by applicable law or agreed to in writing, this
# software is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR
# CONDITIONS OF ANY KIND, either express or implied.  See the License
# for the specific language governing permissions and limitations
# under the License.

##########################################################################################
# INPUT: n/a
# OUTPUT: all subdirectories and files in $SAMPLE except 'init' are copied to $outputDir\$SAMPLE
##########################################################################################

##########################################################################################
# USAGE
##########################################################################################

NGS_USAGE+="Usage: `basename $0` rsync OPTIONS sampleID    --  copy data to analyzed directory\n"

##########################################################################################
# HELP TEXT
##########################################################################################

ngsHelp_RSYNC() {
	echo -e "Usage:\n\t`basename $0` rsync [-o outputDir] sampleID"
	echo -e "Output\n\tall subdirectories in sampleID except 'init' are copied to $ANALYZED\sampleID"
	echo -e "Options:"
	echo -e "\t-o - directory containing subdirectory with analysis files (default: ./analyzed). This is the parent directory of the sample-specific directory. The sampleID will be used to complete the directory path (ie outputDir/sampleID).\n"
	echo -e "Copies all data to 'outputDir/sampleID' directory. This will not copy the files in the sampleID/init directory. Rsync is run twice as a consistency check."
}

##########################################################################################
# LOCAL VARIABLES WITH DEFAULT VALUES. Using the naming convention to
# make sure these variables don't collide with the other modules.
##########################################################################################

ngsLocal_RSYNC_OUT_DIR=$ANALYZED

##########################################################################################
# PROCESSING COMMAND LINE ARGUMENTS
# RSYNC args: sampleID
##########################################################################################

ngsArgs_RSYNC() {
	if [ $# -lt 1 ]; then printHelp "RSYNC"; fi

	# getopts doesn't allow for optional arguments so handle them manually
	while true; do
		case $1 in
			-o) ngsLocal_RSYNC_OUT_DIR=$2
				shift; shift;
				;;
			-*) printf "Illegal option: '%s'\n" "$1"
				printHelp $COMMAND
				exit 0
				;;
 			*) break ;;
		esac
	done
	
	SAMPLE=$1
}

##########################################################################################
# RUNNING COMMAND ACTION
# Copy results to repository.
##########################################################################################

ngsCmd_RSYNC() {
	prnCmd "# BEGIN: COPYING TO REPO"
	
    # we exclude init since that's the unaligned data which is already in the repo. Note that $JOURNAL contains the name of the log file as well as the sample directory. Excluding the '.' from the output directory location will cause the creating of the output directory, if relevant.
	prnCmd "rsync -avh --stats --exclude init --exclude $JOURNAL $SAMPLE $ngsLocal_RSYNC_OUT_DIR/"
	if ! $DEBUG; then 
		rsync -avh --stats --exclude init --exclude $JOURNAL $SAMPLE $ngsLocal_RSYNC_OUT_DIR/
	fi
	
	# the prnCmd is here for proper annotation in the log file. The
	# command is at the end of the function so that we capture all of
	# the prnCmd output.
	prnCmd "cat $JOURNAL >> $ngsLocal_RSYNC_OUT_DIR/$JOURNAL"

	prnCmd "# FINISHED: COPYING TO REPO"
	
	# we run rsync again here to make sure everything copied
	if ! $DEBUG; then 
		rsync -avh --stats --exclude init --exclude $JOURNAL $SAMPLE $ngsLocal_RSYNC_OUT_DIR/.
	fi

	# don't squash existing journal file, so cat onto existing file
	# rather than rsync. This command is at the end of the file since
	# any prnCmd commands would not be captured.
	if ! $DEBUG; then 
		cat $JOURNAL >> $ngsLocal_RSYNC_OUT_DIR/$JOURNAL
	fi
}