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
|
#!/usr/bin/make -f
# -*- makefile -*-
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
export DEB_BUILD_MAINT_OPTIONS=hardening=+all
pkgdata:=microbiomeutil-data
sampledir:=$(CURDIR)/debian/$(pkgdata)/usr/share/doc/$(pkgdata)/examples
%:
dh $@
override_dh_auto_test:
ifneq (,$(findstring nocheck,$(DEB_BUILD_OPTIONS)))
echo 'skip testing due to DEB_BUILD_OPTIONS="$(DEB_BUILD_OPTIONS)"'
else
## Run test suite only on powerfull architectures (amd64) at build time
#ifneq (,$(filter $(DEB_HOST_ARCH),amd64 kfreebsd-amd64))
dh_auto_test
cd ${CURDIR}/ChimeraSlayer/sample_data && $(MAKE) clean
cd ${CURDIR}/NAST-iEr/sample_data && $(MAKE) clean
cd ${CURDIR}/WigeoN/sample_data && $(MAKE) clean
rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx
rm -f formatdb.log
#else
# echo "Do not run test suite when building on architecture $(DEB_HOST_ARCH)"
#endif
endif
override_dh_auto_build:
dh_auto_build
#Pre-make indexes for ChimeraSlayer, otherwise it tries to write them
#to the non-writeable dir on first run and blows up
formatdb -p F -i RESOURCES/rRNA16S.gold.fasta 2>/dev/null
cdbfasta -C RESOURCES/rRNA16S.gold.NAST_ALIGNED.fasta
override_dh_auto_clean:
dh_auto_clean
rm -f RESOURCES/rRNA16S.gold.fasta.n* RESOURCES/*.cidx
rm -f formatdb.log
override_dh_install:
dh_install -XMakefile -Xsample_data -XLICENSE -XNAST-iEr.c
find debian -name '*.pl' -o -name '*.pm' | xargs sed -i 's|/usr/bin/env perl|/usr/bin/perl|g'
override_dh_installexamples:
dh_installexamples
for mod in ChimeraSlayer NAST-iEr WigeoN ; do \
mkdir -p $(sampledir)/$${mod} ; \
cp -a $${mod}/sample_data/* $(sampledir)/$${mod} ; \
sed -i -e "s?../$${mod}?$${mod}?" \
-e "s?^.*\(/util/show_malign_no_gap.pl\)?/usr/lib/NAST-iEr\1?" \
-e "s?^.*\(/run_NAST-iEr.pl\)?/usr/lib/NAST-iEr\1?" \
-e "s?^.*\(ChimeraSlayer.pl\)?/usr/lib/ChimeraSlayer/\1?" \
-e "s?^.*\(/run_WigeoN.pl\)?/usr/lib/WigeoN\1?" \
$(sampledir)/$${mod}/runMe.sh ; \
done
sed -i '1i #!/bin/sh' $(sampledir)/WigeoN/runMe.sh
override_dh_fixperms:
dh_fixperms
find debian -type f -name '*.pm' -print0 | xargs -0r chmod a-x
find debian -type f -name 'genus_counter.pl' -print0 | xargs -0r chmod a+x
|
