#	See instruct: target for how to reproduce the results in this directory.
#	mnoble@broadinstitute.org  2013_03_19
#
#	Also note that:
#		$(Space) contains PANCAN12-AN sample set, which swapped
#							swapped LAML TP samples for TB.
#		awg_pancan12_v46__2013_03_14_copy_frozen is a backup copy
#		of above space, in case this needs to be reproduced "from scratch"
#
#
#  fiss flow_copy Analyses prod awg_pancan12__2013_03_19
#  Copied workflow(s) : [Analyses]
#  fiss flow_copy CopyNumber_Gistic2 prod awg_pancan12__2013_03_19
#  Copied workflow(s) : [CopyNumber_Gistic2]
#  fiss flow_copy Hotnet_Analysis prod awg_pancan12__2013_03_19
#  Copied workflow(s) : [Hotnet_Analysis]
#  fiss flow_copy Mutation_Significance_2.0 prod awg_pancan12__2013_03_19
#  Copied workflow(s) : [Mutation_Significance_2.0]
#  fiss flow_copy Mutation_Significance_CV prod awg_pancan12__2013_03_19
#  Copied workflow(s) : [Mutation_Significance_CV]
#  fiss flow_copy Mutation_Significance_S2N prod awg_pancan12__2013_03_19
#  Copied workflow(s) : [Mutation_Significance_S2N]
#  fiss flow_copy Pathway_Paradigm prod awg_pancan12__2013_03_19
#  Copied workflow(s) : [Pathway_Paradigm]
#  fiss flow_copy stddata prod awg_pancan12__2013_03_19
#  Copied workflow(s) : [stddata]
#
#  fiss stddata_start awg_pancan12__2013_03_19

Diced=/xchip/gdac_data/normalized/loadfiles/normalized
Space=awg_pancan12__2013_03_19
Added=loadfile_added-samples.tsv
Removed=loadfile_removed-samples.tsv
Stamp=normalized.PANCAN12.2013_03_19__18_00_00.samplestamp.txt

instruct:
	@echo "Choose one of:"
	@echo "    make loadfiles"
	@echo "    make samplestamp"
	@echo "    make update_workspace"
	@echo "or combine all 3 together with"
	@echo "    make all"

all:  loadfiles samplestamp update_workspace

loadfiles: $(Added) $(Removed)
samplestamp: $(Diced)/$(Stamp)

$(Diced)/$(Stamp): $(Stamp)
	@echo "Now attempting to copy $(Stamp) to $(Diced), via 'sudo -u gdac'"
	sudo -u gdac cp -f $(Stamp) $(Diced)/.

$(Stamp): xMakeStamp.sh
	sh xMakeStamp.sh > $(Stamp)

$(Added): xAdd.sh
	sh xAdd.sh		>	$(Added)

$(Removed): xRemove.sh
	sh xRemove.sh	>	$(Removed)

update_workspace: $(Stamp) $(Added) $(Removed)
	fiss sample_import $(Space) $(Added)
	fiss sample_import $(Space) $(Removed)
	# Reflect several completely new LAML samples in sset
	# (this pulls in normals, too, but that shouldn't matter)
	fiss sset_import $(Space) LAML-new-samples.sset
	fiss annot_set $(Space) sset=PANCAN12-AN samplestamp $(Diced)/$(Stamp)

clean: 
	\rm -f *~ 

tidy: clean
	\rm -f $(Added) $(Removed)