Attachment #128641 for bug #172499

View | Details | Raw Unified | Return to bug 172499
Collapse All | Expand All

Lines 2-37 Link Here

(-)biology/t_coffee/Makefile (-19 / +23 lines)
2	# $FreeBSD: ports/biology/t_coffee/Makefile,v 1.18 2012/10/01 14:45:16 tabthorpe Exp $	2	# $FreeBSD: ports/biology/t_coffee/Makefile,v 1.18 2012/10/01 14:45:16 tabthorpe Exp $
3		3
4	PORTNAME= t_coffee	4	PORTNAME= t_coffee
5	PORTVERSION= 5.68	5	PORTVERSION= 9.03
		6	DISTVERSIONSUFFIX= .r1318
6	CATEGORIES= biology	7	CATEGORIES= biology
7	MASTER_SITES= http://www.tcoffee.org/Packages/	8	MASTER_SITES= http://www.tcoffee.org/Packages/Stable/%SUBDIR%/
8	DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}	9	MASTER_SITE_SUBDIR= Version_${PORTVERSION}${DISTVERSIONSUFFIX}
		10	DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}${DISTVERSIONSUFFIX}
9		11
10	MAINTAINER= ports@FreeBSD.org	12	MAINTAINER= ports@FreeBSD.org
11	COMMENT= A multiple DNA or protein sequence alignment package	13	COMMENT= A multiple DNA or protein sequence alignment package
12		14
13	BUILD_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw	15	LICENSE= GPLv2
14	RUN_DEPENDS:= ${BUILD_DEPENDS}	16
		17	RUN_DEPENDS= clustalw:${PORTSDIR}/biology/clustalw
		18
		19	OPTIONS_DEFINE= EXAMPLES
15		20
16	BUILD_WRKSRC= ${WRKSRC}/t_coffee_source	21	BUILD_WRKSRC= ${WRKSRC}/t_coffee_source
17	MAKE_ENV= MV=${MV} USER_BIN=${PREFIX}/bin \
18	CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
19		22
		23	USE_FORTRAN= yes
		24	MAKE_ENV= FCC="${FC} ${FFLAGS}"
20	MAKEFILE= makefile	25	MAKEFILE= makefile
		26	MAKE_JOBS_SAFE= yes
21		27
22	do-install:	28	PORTEXAMPLES= *
23	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin	29	PLIST_FILES= bin/TMalign bin/t_coffee
24		30
25	post-install:	31	.include <bsd.port.options.mk>
26	.if !defined(NOPORTDOCS)	32
27	@ ${MKDIR} ${DOCSDIR}/html	33	do-install:
28	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}	34	(cd ${BUILD_WRKSRC} \
29	${INSTALL_DATA} ${WRKSRC}/license.txt ${DOCSDIR}	35	&& ${INSTALL_PROGRAM} TMalign t_coffee ${PREFIX}/bin)
30	${INSTALL_DATA} ${WRKSRC}/html/* ${DOCSDIR}/html	36	.if ${PORT_OPTIONS:MEXAMPLES}
31	.endif	37	@${MKDIR} ${EXAMPLESDIR}
32	.if !defined(NOPORTEXAMPLES)	38	@(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${EXAMPLESDIR})
33	@ ${MKDIR} ${EXAMPLESDIR}
34	cd ${WRKSRC}/example && ${COPYTREE_SHARE} \* ${EXAMPLESDIR}
35	.endif	39	.endif
36		40
37	.include <bsd.port.mk>	41	.include <bsd.port.mk>

Lines 1-2 Link Here

(-)biology/t_coffee/distinfo (-2 / +2 lines)
1	SHA256 (T-COFFEE_distribution_Version_5.68.tar.gz) = 137d188cef6f33a42cbd656482eb961d1588fef3091d2457ee0ef23fab16a6de	1	SHA256 (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c
2	SIZE (T-COFFEE_distribution_Version_5.68.tar.gz) = 2875438	2	SIZE (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 3455629

Lines 1-8 Link Here

(-)biology/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

Line 0 Link Here

(-)biology/t_coffee/files/patch-dev3.c (+10 lines)
	1	--- t_coffee_source/dev3.c.orig 2012-07-13 02:06:31.000000000 +0900
	2	+++ t_coffee_source/dev3.c 2012-10-04 22:14:10.000000000 +0900
	3	@@ -3,6 +3,7 @@
	4	#include <math.h>
	5	#include <stdarg.h>
	6	#include <string.h>
	7	+#include <sys/types.h>
	8	#include <sys/sysctl.h>
	9	#include "dev3_lib_header.h"
	10	/****************************COPYRIGHT NOTICE*****************************/




bin/t_coffee
%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE
%%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt
%%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.doc
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.htm
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.txt
%%PORTDOCS%%%%DOCSDIR%%/license.txt
%%PORTDOCS%%%%DOCSDIR%%/html/t_coffee.html
%%PORTDOCS%%%%DOCSDIR%%/html/t_coffee4html.cgi
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2seqs.fas
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample2.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample3.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample4.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/b30.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/block1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/block2.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cache
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/charge_relay_lib.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/clustalw_method.tc_method
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/command_line.txt
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/error_report.T-COFFEE
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g0.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/x
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g10.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g15.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g5.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/kinases.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/marna.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/new_profile1_pdb1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/new_profile1_pdb1.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/newprf.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/newprf.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p120.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p250
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p350.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf3.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf3.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/seq.fas
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1_1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1_1.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1_1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1_2.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.msf
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln3.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln4.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln5.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.cache
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln7.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln7.cache_aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_dnaseq1.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib1.mocca_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib1.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib2.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib3.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib4.tc_lib02
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib5.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_list1.lib_list
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_param_file.param
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_profile1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_profile2.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_rnaseq1.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq1.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq1.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq2.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq3.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq4.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq5.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq6.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq7.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq8.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree2.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree3.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases.small
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases.small.blosum62mt.sim_file
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_chain.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.code_name
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.coded.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim2_file
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim_file
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta~
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.muscle
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large_muscle_trim.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_oneseq.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_pair.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.b62_aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.cw_aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.expresso
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g0.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g0.cw_aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.cw_aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.score_ascii
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g15.cw_aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.ph
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g15.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.mafft
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.mcoffee
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.muscle
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.probcons
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.score_ascii
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.score_html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.template_file
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small_dna.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc1.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc2.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc3.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc4.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc5.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc6.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc7.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc8.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.html
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.maln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/t_coffee.log
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file.template
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file6.template
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file7.template
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test.lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_lib.tc_lib
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.aln
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.dnd
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.fasta
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.fasta~
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tlara_libraries.tar
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tlara_tRNA_aln10.output
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tlara_tRNA_aln50.output
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tlara_tRNA_aln51.output
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb169168.1
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb89508.1
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/two_profiles.template_file
%%PORTDOCS%%@dirrm %%DOCSDIR%%/html
%%PORTDOCS%%@dirrm %%DOCSDIR%%
%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%

Return to bug 172499

Lines 1-190 Link Here

(-)biology/t_coffee/pkg-plist (-190 lines)
1	bin/t_coffee
2	%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE
3	%%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt
4	%%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt
5	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc
6	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm
7	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt
8	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.doc
9	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.htm
10	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.txt
11	%%PORTDOCS%%%%DOCSDIR%%/license.txt
12	%%PORTDOCS%%%%DOCSDIR%%/html/t_coffee.html
13	%%PORTDOCS%%%%DOCSDIR%%/html/t_coffee4html.cgi
14	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/2seqs.fas
15	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.aln
16	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.dnd
17	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.fasta
18	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d.html
19	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample2.fasta
20	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample3.fasta
21	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/3d_sample4.aln
22	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/b30.aln
23	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/block1.aln
24	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/block2.aln
25	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cache
26	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/charge_relay_lib.tc_lib
27	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/clustalw_method.tc_method
28	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln
29	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln.aln
30	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/combined_aln.aln.html
31	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/command_line.txt
32	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/error_report.T-COFFEE
33	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g0.aln
34	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/x
35	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g10.aln
36	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g15.aln
37	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/g5.aln
38	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/kinases.aln
39	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/marna.tc_lib
40	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/new_profile1_pdb1.aln
41	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/new_profile1_pdb1.html
42	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/newprf.aln
43	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/newprf.html
44	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p120.aln
45	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p250
46	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/p350.aln
47	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.aln
48	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.dnd
49	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf1.fasta
50	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.aln
51	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.dnd
52	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf2.fasta
53	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf3.aln
54	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/prf3.fasta
55	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.aln
56	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.fasta
57	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1.html
58	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/seq.fas
59	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1_1.aln
60	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile1_pdb1_1.html
61	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.aln
62	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.dnd
63	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.fasta
64	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/profile2_pdb2.html
65	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.aln
66	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.dnd
67	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.fasta
68	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1.tc_lib
69	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1_1.aln
70	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln1_2.aln
71	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.aln
72	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.fasta
73	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln2.msf
74	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln3.aln
75	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln4.aln
76	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln5.aln
77	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.aln
78	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.cache
79	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln6.html
80	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln7.aln
81	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_aln7.cache_aln
82	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_dnaseq1.fasta
83	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib1.mocca_lib
84	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib1.tc_lib
85	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib2.tc_lib
86	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib3.tc_lib
87	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib4.tc_lib02
88	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_lib5.tc_lib
89	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_list1.lib_list
90	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_param_file.param
91	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_profile1.aln
92	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_profile2.aln
93	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_rnaseq1.fasta
94	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq1.aln
95	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.aln
96	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq1.fasta
97	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq2.fasta
98	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq3.fasta
99	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq4.fasta
100	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq5.fasta
101	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq6.fasta
102	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq7.fasta
103	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_seq8.seq
104	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree.dnd
105	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree2.dnd
106	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sample_tree3.dnd
107	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases.small
108	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases.small.blosum62mt.sim_file
109	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.aln
110	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.dnd
111	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases1_small.fasta
112	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.aln
113	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.dnd
114	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases2_small.fasta
115	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_chain.fasta
116	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.aln
117	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.code_name
118	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.coded.fasta
119	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.dnd
120	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta
121	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim2_file
122	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim_file
123	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.fasta~
124	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.html
125	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large.muscle
126	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_large_muscle_trim.aln
127	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_oneseq.fasta
128	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_pair.fasta
129	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.aln
130	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.b62_aln
131	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.cw_aln
132	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.dnd
133	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.expresso
134	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.fasta
135	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g0.aln
136	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g0.cw_aln
137	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.cw_aln
138	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.html
139	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g10.score_ascii
140	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g15.cw_aln
141	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.ph
142	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.g15.html
143	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.html
144	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.mafft
145	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.mcoffee
146	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.muscle
147	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.probcons
148	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.score_ascii
149	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.score_html
150	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln
151	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln.aln
152	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.tc_aln.html
153	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small.template_file
154	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sproteases_small_dna.fasta
155	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc1.pdb
156	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc2.pdb
157	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc3.pdb
158	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc4.pdb
159	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc5.pdb
160	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc6.pdb
161	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc7.pdb
162	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/struc8.pdb
163	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.dnd
164	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.fasta
165	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.html
166	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sv.maln
167	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/t_coffee.log
168	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file.template
169	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file6.template
170	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/template_file7.template
171	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test.lib
172	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test.tc_lib
173	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/test_lib.tc_lib
174	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.aln
175	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.dnd
176	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb.fasta
177	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.aln
178	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.dnd
179	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.fasta
180	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/three_pdb_two_seq.fasta~
181	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tlara_libraries.tar
182	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tlara_tRNA_aln10.output
183	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tlara_tRNA_aln50.output
184	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tlara_tRNA_aln51.output
185	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb169168.1
186	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb89508.1
187	%%PORTEXAMPLES%%%%EXAMPLESDIR%%/two_profiles.template_file
188	%%PORTDOCS%%@dirrm %%DOCSDIR%%/html
189	%%PORTDOCS%%@dirrm %%DOCSDIR%%
190	%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%