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Makefile
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CC = gcc
CCFLAGS = -Wall -Wno-parentheses -Wno-sign-compare -Wno-unknown-pragmas
PROGS = annotate_loci \
count2tpm \
expression2gct \
extract_sequence \
make_cls \
make_design_contrast_matrix \
mean \
merge_fastq \
merge_gct \
minmax_gct \
parse_gtf \
reorder_gct \
replace_header_gct \
sort_gct \
subset_gct
B = ./bin
O = ./obj
C = ./csrc
D = ./doc
S = ./scripts
K = /usr/bios-to-go/kern
all: $B $D $(PROGS) doc/tools.md
clean:
for s in $(PROGS) ; do \
/bin/rm -f $B/$$s ; \
done
bin:
mkdir -p $B
# C programs and scripts
annotate_loci: $C/annotate_loci.c $K/plabla.c $K/linestream.c $K/rofutil.c \
$K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $B/annotate_loci
$(CC) $(CCFLAGS) $C/annotate_loci.c -o $B/annotate_loci $K/plabla.c $K/linestream.c \
$K/rofutil.c $K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -I$K
expression2gct: $C/expression2gct.c $K/plabla.c $K/linestream.c $K/rofutil.c \
$K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $B/expression2gct
$(CC) $(CCFLAGS) $C/expression2gct.c -o $B/expression2gct $K/plabla.c $K/linestream.c \
$K/rofutil.c $K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -I$K
extract_sequence: $C/extract_sequence.c $K/plabla.c $K/linestream.c $K/rofutil.c \
$K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $B/extract_sequence
$(CC) $(CCFLAGS) $C/extract_sequence.c -o $B/extract_sequence $K/plabla.c $K/linestream.c \
$K/rofutil.c $K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -I$K
count2tpm: $C/count2tpm.c $K/plabla.c $K/linestream.c $K/rofutil.c $K/array.c \
$K/format.c $K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $(B)/count2tpm
$(CC) $(CCFLAGS) $C/count2tpm.c -o $B/count2tpm $K/plabla.c $K/linestream.c $K/rofutil.c \
$K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -lm -I$K
make_cls: $C/make_cls.c $K/plabla.c $K/linestream.c $K/rofutil.c $K/array.c $K/format.c \
$K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $B/make_cls
$(CC) $(CCFLAGS) $C/make_cls.c -o $B/make_cls $K/plabla.c $K/linestream.c $K/rofutil.c $K/array.c \
$K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -I$K
make_design_contrast_matrix: $C/make_design_contrast_matrix.c $K/plabla.c $K/linestream.c $K/rofutil.c $K/array.c $K/format.c \
$K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $B/make_design_contrast_matrix
$(CC) $(CCFLAGS) $C/make_design_contrast_matrix.c -o $B/make_design_contrast_matrix $K/plabla.c $K/linestream.c $K/rofutil.c $K/array.c \
$K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -I$K
mean: $C/mean.c $K/plabla.c $K/linestream.c $K/rofutil.c $K/array.c \
$K/format.c $K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $(B)/mean
$(CC) $(CCFLAGS) $C/mean.c -o $B/mean $K/plabla.c $K/linestream.c $K/rofutil.c \
$K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -lm -I$K
merge_fastq: $C/merge_fastq.c $K/plabla.c $K/linestream.c $K/rofutil.c $K/format.c $K/array.c \
$K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $B/merge_fastq
$(CC) $(CCFLAGS) $C/merge_fastq.c -o $B/merge_fastq $K/plabla.c $K/linestream.c $K/rofutil.c $K/array.c \
$K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -I$K
merge_gct: $S/merge_gct.sh
cp -p $S/merge_gct.sh $B/merge_gct
chmod +x $B/merge_gct
minmax_gct: $S/minmax_gct.sh
cp -p $S/minmax_gct.sh $B/minmax_gct
chmod +x $B/minmax_gct
parse_gtf: $C/parse_gtf.c $K/plabla.c $K/linestream.c $K/rofutil.c $K/array.c \
$K/format.c $K/log.c $K/arg.c $K/hlrmisc.c
@-/bin/rm -f $(B)/parse_gtf
$(CC) $(CCFLAGS) $C/parse_gtf.c -o $B/parse_gtf $K/plabla.c $K/linestream.c $K/rofutil.c \
$K/array.c $K/format.c $K/log.c $K/arg.c $K/hlrmisc.c -lm -I$K
reorder_gct: $S/minmax_gct.sh
cp -p $S/reorder_gct.sh $B/reorder_gct
chmod +x $B/reorder_gct
replace_header_gct: $S/replace_header_gct.sh
cp -p $S/replace_header_gct.sh $B/replace_header_gct
chmod +x $B/replace_header_gct
sort_gct: $S/sort_gct.sh
cp -p $S/sort_gct.sh $B/sort_gct
chmod +x $B/sort_gct
subset_gct: $S/subset_gct.sh
cp -p $S/subset_gct.sh $B/subset_gct
chmod +x $B/subset_gct
# Make documentation
doc/tools.md: $B $S/make_doc.sh
mkdir -p $D && bash $S/make_doc.sh -b $B -o $D/tools.md