Attachment #62213 for bug #93050




#

PORTNAME=	t_coffee
PORTVERSION=	3.27
CATEGORIES=	biology
MASTER_SITES=	http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}

MAINTAINER=	fernan@iib.unsam.edu.ar
COMMENT=	A multiple DNA or protein sequence alignment package

USE_GCC=	3.3
BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw
RUN_DEPENDS=	${BUILD_DEPENDS}


MAKEFILE=	makefile

do-install:
	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin

post-install:
.if !defined(NOPORTDOCS)
	@ ${MKDIR} ${DOCSDIR}
	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
	@ ${MKDIR} ${EXAMPLESDIR}
	@ cd ${WRKSRC}/example && ${FIND} * \
	  | ${CPIO} --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
	@ ${MKDIR} ${DATADIR}
	${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}
	@ ${MKDIR} ${DATADIR}/html
	${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html
.endif

.include <bsd.port.mk>

.if ${OSVERSION} >= 600000
BROKEN=		"Does not build on FreeBSD >= 6.x"
.endif

.include <bsd.port.post.mk>

Lines 1-3 Link Here

(-)t_coffee/distinfo (-3 / +3 lines)
1	MD5 (T-COFFEE_distribution_Version_3.18.tar.gz) = e671383b9e6b90ded56c615acd2f51c4	1	MD5 (T-COFFEE_distribution_Version_3.27.tar.gz) = 747d907f4b87e07d7b1e670a2b263e23
2	SHA256 (T-COFFEE_distribution_Version_3.18.tar.gz) = e6769bbfecbcd4a00493564ab8e08aefd0d89c7452e5b30114d0d8aec4d36aee	2	SHA256 (T-COFFEE_distribution_Version_3.27.tar.gz) = ffb7920919b24a6144492bec71580cda8a3ef4698acf762f76ebadfcae9aa01a
3	SIZE (T-COFFEE_distribution_Version_3.18.tar.gz) = 1540558	3	SIZE (T-COFFEE_distribution_Version_3.27.tar.gz) = 1295287

Line 0 Link Here

(-)t_coffee/files/patch-Makefile (+8 lines)
	1	--- t_coffee_source/makefile.orig Tue Feb 7 15:11:00 2006
	2	+++ t_coffee_source/makefile Tue Feb 7 15:10:36 2006
	3	@@ -1,4 +1,4 @@
	4	-CC=cc
	5	+#CC=cc
	6	t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_ dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o
	7	$(CC) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_suboptimal_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_ nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o -lm
	8	mv t_coffee ../bin

Return to bug 93050

Lines 7-13 Link Here

(-)t_coffee/Makefile (-12 / +7 lines)
7	#	7	#
8		8
9	PORTNAME= t_coffee	9	PORTNAME= t_coffee
10	PORTVERSION= 3.18	10	PORTVERSION= 3.27
11	CATEGORIES= biology	11	CATEGORIES= biology
12	MASTER_SITES= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/	12	MASTER_SITES= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
13	DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}	13	DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}
Lines 15-20 Link Here
15	MAINTAINER= fernan@iib.unsam.edu.ar	15	MAINTAINER= fernan@iib.unsam.edu.ar
16	COMMENT= A multiple DNA or protein sequence alignment package	16	COMMENT= A multiple DNA or protein sequence alignment package
17		17
		18	USE_GCC= 3.3
18	BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw	19	BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw
19	RUN_DEPENDS= ${BUILD_DEPENDS}	20	RUN_DEPENDS= ${BUILD_DEPENDS}
20		21
Lines 25-49 Link Here
25	MAKEFILE= makefile	26	MAKEFILE= makefile
26		27
27	do-install:	28	do-install:
28	@ ${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin	29	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
29		30
30	post-install:	31	post-install:
31	.if !defined(NOPORTDOCS)	32	.if !defined(NOPORTDOCS)
32	@ ${MKDIR} ${DOCSDIR}	33	@ ${MKDIR} ${DOCSDIR}
33	@ ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}	34	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
34	@ ${MKDIR} ${EXAMPLESDIR}	35	@ ${MKDIR} ${EXAMPLESDIR}
35	@ cd ${WRKSRC}/example && ${FIND} * \	36	@ cd ${WRKSRC}/example && ${FIND} * \
36	\| ${CPIO} --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}	37	\| ${CPIO} --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
37	@ ${MKDIR} ${DATADIR}	38	@ ${MKDIR} ${DATADIR}
38	@ ${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}	39	${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}
39	@ ${MKDIR} ${DATADIR}/html	40	@ ${MKDIR} ${DATADIR}/html
40	@ ${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html	41	${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html
41	.endif	42	.endif
42		43
43	.include <bsd.port.pre.mk>	44	.include <bsd.port.mk>
44
45	.if ${OSVERSION} >= 600000
46	BROKEN= "Does not build on FreeBSD >= 6.x"
47	.endif
48
49	.include <bsd.port.post.mk>