1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
|
#!/usr/bin/make -f
# Uncomment this to turn on verbose mode.
# export DH_VERBOSE = 1
export DEB_BUILD_MAINT_OPTIONS = hardening=+all
export DEB_CFLAGS_MAINT_APPEND = -Wall -pedantic -std=gnu17
PACKAGE:=sift
DESTDIR:=$(CURDIR)/debian/$(PACKAGE)
VERSION:=6.2.1
prefix:=/usr
pkgdatadir:=$(prefix)/share/$(PACKAGE)
SIFT_BINDIR := $(prefix)/lib/sift/bin
SIFT_SCRIPTDIR := $(prefix)/lib/sift/bin
parallel := 1
ifneq (,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
parallel = $(patsubst parallel=%,%,$(filter parallel=%,$(DEB_BUILD_OPTIONS)))
endif
%:
dh $@
MAN1:=info_on_seqs.1 SIFT_for_submitting_fasta_seq.csh.1
.PHONY: man
man: $(MAN1)
%.1: %.pod
pod2man -c 'User Commands' --release="$(VERSION)" $< > $@
override_dh_auto_clean:
if [ -e src/Makefile -a -e src/deps.mk ]; then make -j$(parallel) -C src prefix=$(prefix) distclean; fi
rm -f $(MAN1)
# remove pre-compiled binaries from bin - thanks to Michael Bienia <geser@ubuntu.com>
rm -f bin/choose_seqs_via_psiblastseedmedian
rm -f bin/clump_output_alignedseq
rm -f bin/consensus_to_seq
rm -f bin/fastaseqs
rm -f bin/info_on_seqs
rm -f bin/process_alignment
rm -f bin/psiblast_res_to_fasta_dbpairwise
rm -f bin/seqs_from_psiblast_res
rm -f src/choose_seqs_via_psiblastseedmedian
rm -f src/clump_output_alignedseq
rm -f src/consensus_to_seq
rm -f src/deps.mk
rm -f src/info_on_seqs
rm -f src/psiblast_res_to_fasta_dbpairwise
rm -f src/seqs_from_psiblast_res
find . -name "*.o" -delete
override_dh_auto_build: man
make -j$(parallel) -C src prefix=$(prefix) VERSION=$(VERSION) deps.mk && \
make -j$(parallel) -C src prefix=$(prefix) VERSION=$(VERSION)
override_dh_auto_install:
make -C src DESTDIR=$(DESTDIR) prefix=$(prefix) install
override_dh_install:
# lkajan: fastaseqs comes from the blimps package, this source does not have rules for creating it
dh_install -X.svn -X.swp -XIntersectFeatures.jar -XManuals -Xfastaseqs -Xlinux -Xsolaris bin $(prefix)/lib/sift/
#dh_install bin/IntersectFeatures.jar $(pkgdatadir)/
dh_install -X.svn -X.swp blimps/docs $(prefix)/share/sift/blimps/
#Links are created by debian/links
for f in SIFT_for_submitting_fasta_seq.csh SIFT_for_submitting_NCBI_gi_id.csh; do \
sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \
done;
for f in seqs_chosen_via_median_info.csh \
SIFT_for_submitting_fasta_seq.csh \
SIFT_for_submitting_NCBI_gi_id.csh; \
do \
sed --in-place -e 's|\b__MAKE_PREFIX__\b|$(prefix)|g;s|__SIFT_SCRIPTDIR__|$(SIFT_SCRIPTDIR)|g;s|__SIFT_BINDIR__|$(SIFT_BINDIR)|g;' $(DESTDIR)$(SIFT_SCRIPTDIR)/$$f; \
done;
# look out: DNA_PROT_SUBROUTINES.pl is really a module (should be pm)!
# Update: Not existing at all in 6.2.1
for f in SIFT_subroutines.pm \
DNA_PROT_SUBROUTINES.pl \
perlscripts/get_BLINK_seq.pl \
perlscripts/separate_query_from_rest_of_seqs.pl \
perlscripts/separate_query_from_database.pl; \
do \
ff="$(DESTDIR)$(prefix)/lib/sift/bin/$$f"; \
if [ -r "$$ff" ]; then \
sed -i '1s%/usr/local/bin/%/usr/bin/%' $$ff; \
chmod +x $$ff; \
fi; \
done;
for f in IntersectFeatures.jar; do \
if [ -r "$(DESTDIR)$(pkgdatadir)/$$f" ]; then \
chmod -x $(DESTDIR)$(pkgdatadir)/$$f; \
fi; \
done;
|
