Attachment #195047 for bug #229693

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# $FreeBSD$

PORTNAME=	hmmer
PORTVERSION=	3.2.1
CATEGORIES=	biology
MASTER_SITES=	http://eddylab.org/software/hmmer/

MAINTAINER=	mzaki@niid.go.jp
COMMENT=	Profile hidden Markov models for biological sequence analysis

LICENSE=	BSD3CLAUSE
LICENSE_FILE=	${WRKSRC}/LICENSE

ONLY_FOR_ARCHS=	amd64 i386 ia64 powerpc powerpc64
ONLY_FOR_ARCHS_REASON=	requires SSE2 or AltiVec instructions

USES=		gmake perl5 shebangfix

GNU_CONFIGURE=	yes
MAKE_ARGS=	V=1

TEST_TARGET=	check
USE_PERL5=	test
SHEBANG_GLOB=	*.pl
SHEBANG_FILES=	easel/devkit/*

OPTIONS_DEFINE=	DOCS EXAMPLES TEST
TEST_TEST_TARGET=	check
TEST_USES=	shebangfix perl5
TEST_VARS=	shebang_glob=*.pl shebang_files=easel/devkit/* use_perl5=build

DOCFILES=	Userguide.pdf
EXAMPLES=	7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
		Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \
		globins4.hmm globins4.sto globins45.fa
		minifam minifam.h3f minifam.h3i minifam.h3m minifam.h3p

TEST_VARS=	use_perl5=build

post-build-TEST-on:	do-test

post-install:

Lines 1-3 Link Here

(-)distinfo (-3 / +3 lines)
1	TIMESTAMP = 1510218548	1	TIMESTAMP = 1531293655
2	SHA256 (hmmer-3.1b2.tar.gz) = dd16edf4385c1df072c9e2f58c16ee1872d855a018a2ee6894205277017b5536	2	SHA256 (hmmer-3.2.1.tar.gz) = a56129f9d786ec25265774519fc4e736bbc16e4076946dcbd7f2c16efc8e2b9c
3	SIZE (hmmer-3.1b2.tar.gz) = 5965253	3	SIZE (hmmer-3.2.1.tar.gz) = 7670274

Lines 1-10 Link Here

(-)files/patch-configure (-10 lines)
1	--- configure.orig 2015-02-26 12:45:55 UTC
2	+++ configure
3	@@ -3912,6 +3912,7 @@ fi
4	if test "$impl_choice" = "none"; then
5	case $host in
6	ia64--) impl_choice=sse;;
7	+ amd64--) impl_choice=sse;;
8	i?86--) impl_choice=sse;;
9	x86--*) impl_choice=sse;;
10	powerpc--*) impl_choice=vmx;;




bin/alimask
bin/hmmalign
bin/hmmbuild
bin/hmmc2
bin/hmmconvert
bin/hmmemit
bin/hmmerfm-exactmatch
bin/hmmfetch
bin/hmmlogo
bin/hmmpgmd

bin/nhmmer
bin/nhmmscan
bin/phmmer
include/cachedb.h
include/hmmer.h
include/impl_sse.h
include/p7_config.h
include/p7_gbands.h
include/p7_gmxb.h
include/p7_gmxchk.h
include/p7_hmmcache.h
lib/libhmmer.a
man/man1/alimask.1.gz
man/man1/hmmalign.1.gz
man/man1/hmmbuild.1.gz

man/man1/nhmmer.1.gz
man/man1/nhmmscan.1.gz
man/man1/phmmer.1.gz
%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.out
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p

Return to bug 229693

Lines 2-32 Link Here

(-)Makefile (-12 / +19 lines)
2	# $FreeBSD$	2	# $FreeBSD$
3		3
4	PORTNAME= hmmer	4	PORTNAME= hmmer
5	PORTVERSION= 3.1b2	5	PORTVERSION= 3.2.1
6	CATEGORIES= biology	6	CATEGORIES= biology
7	MASTER_SITES= http://eddylab.org/software/hmmer3/${PORTVERSION}/	7	MASTER_SITES= http://eddylab.org/software/hmmer/
8		8
9	MAINTAINER= mzaki@niid.go.jp	9	MAINTAINER= mzaki@niid.go.jp
10	COMMENT= Profile hidden Markov models for biological sequence analysis	10	COMMENT= Profile hidden Markov models for biological sequence analysis
11		11
12	LICENSE= GPLv3	12	LICENSE= BSD3CLAUSE
13	LICENSE_FILE= ${WRKSRC}/LICENSE	13	LICENSE_FILE= ${WRKSRC}/LICENSE
14		14
15	USES= gmake	15	ONLY_FOR_ARCHS= amd64 i386 ia64 powerpc powerpc64
		16	ONLY_FOR_ARCHS_REASON= requires SSE2 or AltiVec instructions
		17
		18	USES= gmake perl5 shebangfix
		19
16	GNU_CONFIGURE= yes	20	GNU_CONFIGURE= yes
17	MAKE_ARGS= V=1	21	MAKE_ARGS= V=1
18		22
		23	TEST_TARGET= check
		24	USE_PERL5= test
		25	SHEBANG_GLOB= *.pl
		26	SHEBANG_FILES= easel/devkit/*
		27
19	OPTIONS_DEFINE= DOCS EXAMPLES TEST	28	OPTIONS_DEFINE= DOCS EXAMPLES TEST
20	TEST_TEST_TARGET= check
21	TEST_USES= shebangfix perl5
22	TEST_VARS= shebang_glob=.pl shebang_files=easel/devkit/ use_perl5=build
23		29
24	DOCFILES= COPYRIGHT Userguide.pdf	30	DOCFILES= Userguide.pdf
25	EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.out MADE1.sto \	31	EXAMPLES= 7LESS_DROME HBB_HUMAN MADE1.hmm MADE1.sto \
26	Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.out fn3.sto \	32	Pkinase.hmm Pkinase.sto dna_target.fa fn3.hmm fn3.sto \
27	globins4.hmm globins4.out globins4.sto globins45.fa \	33	globins4.hmm globins4.sto globins45.fa
28	minifam minifam.h3f minifam.h3i minifam.h3m minifam.h3p
29		34
		35	TEST_VARS= use_perl5=build
		36
30	post-build-TEST-on: do-test	37	post-build-TEST-on: do-test
31		38
32	post-install:	39	post-install:

Lines 1-10 Link Here

(-)pkg-plist (-20 lines)
1	bin/alimask	1	bin/alimask
2	bin/hmmalign	2	bin/hmmalign
3	bin/hmmbuild	3	bin/hmmbuild
4	bin/hmmc2
5	bin/hmmconvert	4	bin/hmmconvert
6	bin/hmmemit	5	bin/hmmemit
7	bin/hmmerfm-exactmatch
8	bin/hmmfetch	6	bin/hmmfetch
9	bin/hmmlogo	7	bin/hmmlogo
10	bin/hmmpgmd	8	bin/hmmpgmd
Lines 18-32 Link Here
18	bin/nhmmer	16	bin/nhmmer
19	bin/nhmmscan	17	bin/nhmmscan
20	bin/phmmer	18	bin/phmmer
21	include/cachedb.h
22	include/hmmer.h
23	include/impl_sse.h
24	include/p7_config.h
25	include/p7_gbands.h
26	include/p7_gmxb.h
27	include/p7_gmxchk.h
28	include/p7_hmmcache.h
29	lib/libhmmer.a
30	man/man1/alimask.1.gz	19	man/man1/alimask.1.gz
31	man/man1/hmmalign.1.gz	20	man/man1/hmmalign.1.gz
32	man/man1/hmmbuild.1.gz	21	man/man1/hmmbuild.1.gz
Lines 46-70 Link Here
46	man/man1/nhmmer.1.gz	35	man/man1/nhmmer.1.gz
47	man/man1/nhmmscan.1.gz	36	man/man1/nhmmscan.1.gz
48	man/man1/phmmer.1.gz	37	man/man1/phmmer.1.gz
49	%%PORTDOCS%%%%DOCSDIR%%/COPYRIGHT
50	%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf	38	%%PORTDOCS%%%%DOCSDIR%%/Userguide.pdf
51	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME	39	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/7LESS_DROME
52	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN	40	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/HBB_HUMAN
53	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm	41	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.hmm
54	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.out
55	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto	42	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/MADE1.sto
56	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm	43	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.hmm
57	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto	44	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/Pkinase.sto
58	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa	45	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dna_target.fa
59	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm	46	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.hmm
60	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.out
61	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto	47	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/fn3.sto
62	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm	48	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.hmm
63	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.out
64	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto	49	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins4.sto
65	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa	50	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/globins45.fa
66	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam
67	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3f
68	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3i
69	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3m
70	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/minifam.h3p