# run agree 
#
#   Command file for running agree for the best sets of (p,l) values found
#   by the analysis. These data are represented in the blocks in Fig 4A, B, C
#   of the "Comparison of five methods..." (Stojanovic et al) paper.
#
#   In the end, run_araCe produces the file of plain landmarks (list-formatted
#   output of agree for the best (p,l) values for this region, to be used in
#   displaying the alignment boxes with llat/maps (similar to Fig. 5 of
#   the "Comparison..." paper). Absolute paths for the files might change.
#

all:
	run_agree
	run_cluster
	run_expand
	run_mv

run_agree:
	ln -s /net/finch/usr/local/globin/bin/agree .
	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 13 -a 3 -x \
	-p 60 > agree.hs2.X.l13.p60.list
	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 14 -a 3 -x \
	-p 60 > agree.hs2.X.l14.p60.list
	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 15 -a 3 -x \
	-p 60 > agree.hs2.X.l15.p60.list
	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 16 -a 3 -x \
	-p 60 > agree.hs2.X.l16.p60.list
	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 17 -a 3 -x \
	-p 60 > agree.hs2.X.l17.p60.list
	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 18 -a 3 -x \
	-p 60 > agree.hs2.X.l18.p60.list
	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 11240 11510 -l 19 -a 3 -x \
	-p 60 > agree.hs2.X.l19.p60.list


	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 7188 7487 -l 4 -a 3 -x \
	-p 100 > agree.hs3.X.l4.p100.list

	agree alignment -I /usr/local/globin/data/align.beta  \
	-r 64561 64826 -l 6 -a 3 -x \
	-p 80 > agree.beta.X.l6.p80.list


run_cluster:
	ln -s ../tools/cluster .
	cluster agree.hs2.X.l13.p60.list > agree.hs2.X.l13.p60.c
	cluster agree.hs2.X.l14.p60.list > agree.hs2.X.l14.p60.c
	cluster agree.hs2.X.l15.p60.list > agree.hs2.X.l15.p60.c
	cluster agree.hs2.X.l16.p60.list > agree.hs2.X.l16.p60.c
	cluster agree.hs2.X.l17.p60.list > agree.hs2.X.l17.p60.c
	cluster agree.hs2.X.l18.p60.list > agree.hs2.X.l18.p60.c
	cluster agree.hs2.X.l19.p60.list > agree.hs2.X.l19.p60.c
	cluster agree.hs3.X.l4.p100.list > agree.hs3.X.l4.p100.c
	cluster agree.beta.X.l6.p80.list > agree.beta.X.l6.p80.c
	rm cluster

run_expand:
	ln -s ../tools/expand .
	expand agree.hs2.X.l13.p60.c > agree.hs2.X.l13.p60.graph
	expand agree.hs2.X.l14.p60.c > agree.hs2.X.l14.p60.graph
	expand agree.hs2.X.l15.p60.c > agree.hs2.X.l15.p60.graph 
	expand agree.hs2.X.l16.p60.c > agree.hs2.X.l16.p60.graph
	expand agree.hs2.X.l17.p60.c > agree.hs2.X.l17.p60.graph
	expand agree.hs2.X.l18.p60.c > agree.hs2.X.l18.p60.graph
	expand agree.hs2.X.l19.p60.c > agree.hs2.X.l19.p60.graph
	expand agree.hs3.X.l4.p100.c > agree.hs3.X.l4.p100.graph
	expand agree.beta.X.l6.p80.c > agree.beta.X.l6.p80.graph
	rm expand

run_mv:
	mv agree.hs2.*.c ../../results/hs2
	mv agree.hs2.*.graph ../../results/hs2
	mv agree.hs3.*.c ../../results/hs3
	mv agree.hs3.*.graph ../../results/hs3
	mv agree.beta.*.c ../../results/beta
	mv agree.beta.*.graph ../../results/beta


run_araCe:
	/net/finch/usr/local/globin/bin/agree araCe.a -I \
	/home/galapagos/florea/test.d -l 8 -a 5 -x \
	-p 90 > tmp
	mv tmp /home/galapagos/florea/promoter.d/align.d/agree.araCe.X.l8.p90.list