################################################################################
##
## 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 FlowCellTargets.mk
##
## brief Standard make targets for the whole flow cell.
##
## postrun, reporting, summaries, clean, etc.
##
## author Come Raczy
##
################################################################################
# declare everything as secondary so that cleaning unnecessary files does not 
# cause rebuild of everything. BREAKS PATTERN RULES WITH QMAKE!
#.SECONDARY:

include $(MAKEFILES_DIR)/FlowcellSummary.mk
include $(MAKEFILES_DIR)/Report.mk

$(TOOLS):
	$(ECHO) Could not find program $@ $(AND) $(EXIT) $(ERROR_MISSING_PROGRAM)

self_test: shell_test.done

shell_test.done: has_shell.done has_pipefail.done

has_shell.done: override OLD_SHELL:=$(SHELL)
has_shell.done: override SHELL:=/bin/sh
has_shell.done:
	@[ -e $(word 1, $(OLD_SHELL)) ] || { echo invalid shell: $(word 1, $(OLD_SHELL)): not found ; exit 1 ; }
	@[ -x $(word 1, $(OLD_SHELL)) ] || { echo invalid shell: $(word 1, $(OLD_SHELL)): not executable ; exit 1 ; }

LIST_SHELL_OPTIONS ?= $(SET) -o
CHECK_PIPEFAIL ?= { $(LIST_SHELL_OPTIONS) | $(GREP) pipefail ; }
has_pipefail.done: has_shell.done
	@$(LIST_SHELL_OPTIONS) > /dev/null || { $(ECHO) ; $(ECHO) Error: could not list shell options: $(LIST_SHELL_OPTIONS) \(SHELL=$(SHELL)\) ; $(ECHO) Disable "'pipefail'" check by setting the environment variable ; $(ECHO) LIST_SHELL_OPTIONS to \"echo pipefail on\" ; exit $(ERROR_NO_PIPEFAIL) ; }
	@$(CHECK_PIPEFAIL) > /dev/null || { $(ECHO) ; $(ECHO) Error: Shell does not support "'pipefail'" \(SHELL=$(SHELL)\) ; $(ECHO) "'pipefail'" is required for accurate workflow management ; $(ECHO) Disable "'pipefail'" check by setting the environment variable ; $(ECHO) LIST_SHELL_OPTIONS to \"echo pipefail on\" ; exit ${ERROR_NO_PIPEFAIL} ; }
	@{ $(CHECK_PIPEFAIL) | grep '\<on\>' ; } > /dev/null || { $(ECHO) ; $(ECHO) Error: Shell option "'pipefail'" is not set \(SHELL=$(SHELL)\) ; $(ECHO) Try \'SHELL=\"$(SHELL) -o pipefail\"\' on the make command line ; $(ECHO) Disable "'pipefail'" check by setting the environment variable ; $(ECHO) LIST_SHELL_OPTIONS to \"echo pipefail on\" ; exit ${ERROR_NO_PIPEFAIL} ; }

clean_intermediate.done: postrun.done
	$(if $(call IS_BOOLEAN_TRUE, $(KEEP_INTERMEDIARY)), , $(FIND) $(TEMP_DIR) -type f -not -name .sentinel |xargs $(RM))

clean:
	$(FIND) $(TEMP_DIR) -type f -not -name .sentinel |xargs $(RM) $(AND) @echo Finished cleaning.

recursive_msg.done:
	@echo No target \'recursive\' - using \'all\' instead.

recursive: recursive_msg.done all