################################################################################
##
## Copyright (c) 2007-2011 Illumina, Inc.
##
## This software is covered by the "Illumina Genome Analyzer Software 
## License Agreement" and the "Illumina Source Code License Agreement", 
## and certain third party copyright/licenses, and any user of this 
## source file is bound by the terms therein (see accompanying files
## Illumina_Genome_Analyzer_Software_License_Agreement.pdf and
## Illumina_Source_Code_License_Agreement.pdf and third party 
## copyright/license notices).
##
## This file is part of the Consensus Assessment of Sequence And VAriation
## (CASAVA) software package.
##
## file Makefile
##
## brief Master makefile to copy into the analysis directory.
##
## This Makefile has the rules to build the lane specific makefiles containing
## the variable definitions for each lane.
##
## author Come Raczy
##
################################################################################

# first target needs to be defined in the beginning. Ohterwise includes such as
# Log.mk cause unexpected behavior
firsttarget: default

# Location where the static makefiles are located
MAKEFILES_DIR:=@CASAVA_FULL_DATADIR@/makefiles

# Full path to the sample sheet
SAMPLE_SHEET:=SampleSheet.csv

# Import the global configuration
include $(MAKEFILES_DIR)/Config.mk

include $(MAKEFILES_DIR)/Sentinel.mk

# Make sure this is declared before the inclusion of Log.mk
# Log.mk heavily messess with SHELL. This casues many misunderstanding within
# make when it tries to rebuild outdated includes. Just postpone tricks until
# after the includes are in order. Preserve SHELL for recipe
Makefiles/config.mk: SHELL:=$(SHELL)
Makefiles/config.mk: $(SAMPLE_SHEET) Makefiles/.sentinel
	$(LIBEXEC_CONFIGURE_ALIGNMENT) --sample-sheet $< > $(SAFEPIPETARGET)

# Import the configuration for the current analysis folder
include Makefiles/config.mk

# Import the logging functionalities
include $(MAKEFILES_DIR)/Log.mk

# Import the debug functionalities
include $(MAKEFILES_DIR)/Debug.mk

all: clean_intermediate.done

# Import the project navigation framework
include $(MAKEFILES_DIR)/AnalyseProjects.mk

# Import the global flow-cell targets
include $(MAKEFILES_DIR)/FlowCellTargets.mk

# Add the target for the alignment of the first read
r1 : $(r1_eland_extended)

default: all