blob: 2932bde5f752e3faf5d130dad5bd9098f8798cab (
plain)
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
|
# $NetBSD: Makefile,v 1.29 2022/04/18 19:10:27 adam Exp $
DISTNAME= ncbi-blast-2.13.0+-src
PKGNAME= ${DISTNAME:S/+-src//:S/blast/blast+/}
PKGREVISION= 1
CATEGORIES= biology
MASTER_SITES= https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ \
https://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${PKGVERSION_NOREV}/
MAINTAINER= bacon@NetBSD.org
HOMEPAGE= http://blast.ncbi.nlm.nih.gov/
COMMENT= NCBI implementation of Basic Local Alignment Search Tool
LICENSE= public-domain
# Fix "undefined _ThreadRuneLocale" error on FreeBSD 10.0
# Fix "unknown options" in configure
SUBST_CLASSES+= configure
SUBST_STAGE.configure= pre-configure
SUBST_SED.configure+= -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_INTERNAL|'
SUBST_SED.configure+= -e '/--infodir=DIR/d'
SUBST_SED.configure+= -e '/--mandir=DIR/d'
SUBST_FILES.configure+= src/build-system/configure
USE_TOOLS+= bash gmake perl
USE_LANGUAGES= c c++
GNU_CONFIGURE= yes
GNU_CONFIGURE_STRICT= no # doesn't know --enable-option-checking
REPLACE_BASH= scripts/common/impl/define_random_macros.sh
REPLACE_BASH+= src/app/blast/get_species_taxids.sh
REPLACE_PERL= src/app/blast/legacy_blast.pl src/app/blast/update_blastdb.pl
REPLACE_PYTHON= src/app/winmasker/windowmasker_2.2.22_adapter.py
REPLACE_PYTHON+= src/app/blast/cleanup-blastdb-volumes.py
MKPIE_SUPPORTED= no # Temporary fix
# The test for amq can hang, but amq is not needed so just avoid the test
# configure chooses /usr/local/bin/ar with no flags
# Resolve a conflict with libproj by moving libs to a subdir
CONFIGURE_ENV= ncbi_cv_prog_amq_w=no
CONFIGURE_ARGS+= AR="ar cr" --without-boost
CONFIGURE_ARGS+= --libdir=${PREFIX}/lib/ncbi-tools++
WRKSRC= ${WRKDIR}/${DISTNAME}/c++
.include "../../mk/bsd.prefs.mk"
.if ${OPSYS} == NetBSD
# statfs is deprecated on NetBSD, but still exists in libc
# configure checks only for undefined reference, not for usability
CONFIGURE_ENV+= ac_cv_func_statfs=no
.endif
.if ${OPSYS} == Darwin
CONFIGURE_ARGS+= --without-openmp
.endif
# c++/src/objtools/edit/seq_entry_edit.cpp: In member function 'void ncbi::objects::edit::{anonymous}::CSeqdescSortMap::Init()':
# c++/src/objtools/edit/seq_entry_edit.cpp:172:44: error: array subscript has type 'char' [-Werror=char-subscripts]
# while (descr_insert_order[index] != 0)
# Maybe fix this later.
BUILDLINK_TRANSFORM+= rm:-Werror=char-subscripts
post-install:
${RM} ${DESTDIR}${PREFIX}/include/ncbi-tools++/*/*/.cvsignore.extra
.if ${OPSYS} != Darwin
${STRIP} ${DESTDIR}${PREFIX}/lib/ncbi-tools++/*.so
.endif
.include "../../devel/zlib/buildlink3.mk"
.include "../../archivers/lzo/buildlink3.mk"
.include "../../archivers/bzip2/buildlink3.mk"
.include "../../devel/pcre/buildlink3.mk"
.include "../../databases/lmdb/buildlink3.mk"
.include "../../security/gnutls/buildlink3.mk"
.include "../../devel/gmp/buildlink3.mk"
.include "../../devel/libidn2/buildlink3.mk"
.include "../../security/nettle/buildlink3.mk"
.include "../../security/libtasn1/buildlink3.mk"
.include "../../security/p11-kit/buildlink3.mk"
.include "../../security/libgcrypt/buildlink3.mk"
.include "../../databases/sqlite3/buildlink3.mk"
.include "../../security/libgpg-error/buildlink3.mk"
.include "../../lang/python/application.mk"
.include "../../mk/bsd.pkg.mk"
|
