Attachment #57856 for bug #87264

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# ex:ts=8
# New ports collection makefile for:	t_coffee
# Date created:		27 June 2001
# Whom:	      		Johann Visagie <wjv@FreeBSD.org>

#

PORTNAME=	t_coffee
PORTVERSION=	3.14
CATEGORIES=	biology
MASTER_SITES=	http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}

		CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw

MAKEFILE=	makefile
SCRIPTS=	msf_aln2fasta_aln.pl blast_aln2fasta_aln.pl \
		fasta_aln2fasta_aln_unique_name.pl extract_from_pdb \
		fugue_client t_coffee_dpa t_coffee_dpa2 mocca

do-install:
	@ ${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
.for scriptfile in ${SCRIPTS}
	@ ${INSTALL_SCRIPT} ${WRKSRC}/bin/${scriptfile} ${PREFIX}/bin
.endfor

post-install:
.if !defined(NOPORTDOCS)
	@ ${MKDIR} ${DOCSDIR}
	@ ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
	@ ${MKDIR} ${EXAMPLESDIR}
	@ ${RMDIR} ${WRKSRC}/example/aln 2>/dev/null || ${TRUE}
	@ 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>

Lines 1-2 Link Here

(-)t_coffee/distinfo (-2 / +2 lines)
1	MD5 (T-COFFEE_distribution_Version_2.03.tar.gz) = a86e2d83c17058b03be0170566d634f0	1	MD5 (T-COFFEE_distribution_Version_3.14.tar.gz) = ad467933434fbe7137b08aea30a79922
2	SIZE (T-COFFEE_distribution_Version_2.03.tar.gz) = 864853	2	SIZE (T-COFFEE_distribution_Version_3.14.tar.gz) = 1533171

Lines 16-21 Link Here

(-)t_coffee/pkg-descr (-1 / +1 lines)
16	407-422,1998	16	407-422,1998
17		17
18	Author: Cedric Notredame <cedric.notredame@europe.com>	18	Author: Cedric Notredame <cedric.notredame@europe.com>
19	WWW: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html	19	WWW: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
20		20
21	-- Johann Visagie <wjv@FreeBSD.org>	21	-- Johann Visagie <wjv@FreeBSD.org>




bin/t_coffee
bin/msf_aln2fasta_aln.pl
bin/blast_aln2fasta_aln.pl
bin/fasta_aln2fasta_aln_unique_name.pl
bin/extract_from_pdb
bin/fugue_client
bin/t_coffee_dpa
bin/t_coffee_dpa2
bin/mocca
%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE
%%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt
%%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt
%%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf
%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.txt
%%EXAMPLESDIR%%/3d.fasta
%%EXAMPLESDIR%%/3d_sample2.fasta
%%EXAMPLESDIR%%/3d_sample3.fasta
%%EXAMPLESDIR%%/clustalw_method.tc_method
%%EXAMPLESDIR%%/command_line.txt
%%EXAMPLESDIR%%/error_report.T-COFFEE.3752
%%EXAMPLESDIR%%/sample_aln1.aln
%%EXAMPLESDIR%%/sample_aln1.fasta
%%EXAMPLESDIR%%/sample_aln1.tc_lib
%%EXAMPLESDIR%%/sample_aln1_1.aln
%%EXAMPLESDIR%%/sample_aln1_2.aln
%%EXAMPLESDIR%%/sample_aln2.aln
%%EXAMPLESDIR%%/sample_aln2.fasta
%%EXAMPLESDIR%%/sample_aln2.msf
%%EXAMPLESDIR%%/sample_aln3.aln
%%EXAMPLESDIR%%/sample_aln4.aln
%%EXAMPLESDIR%%/sample_dnaseq1.fasta
%%EXAMPLESDIR%%/struc1.pdb
%%EXAMPLESDIR%%/sample_lib1.mocca_lib
%%EXAMPLESDIR%%/sample_lib1.tc_lib
%%EXAMPLESDIR%%/sample_lib2.tc_lib
%%EXAMPLESDIR%%/sample_lib3.tc_lib
%%EXAMPLESDIR%%/sample_lib4.tc_lib02
%%EXAMPLESDIR%%/sample_list1.lib_list
%%EXAMPLESDIR%%/sample_param_file.param
%%EXAMPLESDIR%%/sample_profile1.aln
%%EXAMPLESDIR%%/sample_profile2.aln
%%EXAMPLESDIR%%/sample_seq1.aln
%%EXAMPLESDIR%%/sample_seq1.fasta
%%EXAMPLESDIR%%/sample_seq2.fasta
%%EXAMPLESDIR%%/sample_seq3.fasta
%%EXAMPLESDIR%%/sample_seq4.fasta
%%EXAMPLESDIR%%/sample_seq5.fasta
%%EXAMPLESDIR%%/sample_tree.dnd
%%EXAMPLESDIR%%/struc2.pdb
%%EXAMPLESDIR%%/struc3.pdb
%%EXAMPLESDIR%%/struc4.pdb
%%EXAMPLESDIR%%/t_coffee.log
%%EXAMPLESDIR%%/template_file.template
%%EXAMPLESDIR%%/test.lib
%%EXAMPLESDIR%%/test.tc_lib
%%EXAMPLESDIR%%/test_lib.tc_lib
%%DATADIR%%/license.txt
%%DATADIR%%/html/t_coffee.html
%%DATADIR%%/html/t_coffee4html.cgi
%%PORTDOCS%% @dirrm %%DOCSDIR%%/t_coffee
@unexec rmdir %D/%%DOCSDIR%% 2>/dev/null || true
@dirrm %%EXAMPLESDIR%%/t_coffee
@unexec rmdir %D/%%EXAMPLESDIR%% 2>/dev/null || true
@dirrm %%DATADIR%%/html
@unexec rmdir %D/%%DATADIR%% 2>/dev/null || true
%%EXAMPLESDIR%%/seq/1lkl_ref4.pep
%%EXAMPLESDIR%%/seq/1lvl_ref1.pep
%%EXAMPLESDIR%%/seq/1lvl_ref2.pep
%%EXAMPLESDIR%%/seq/1mfa_ref4.pep
%%EXAMPLESDIR%%/seq/1mrj_ref1.pep
%%EXAMPLESDIR%%/seq/1pamA_ref1.pep
%%EXAMPLESDIR%%/seq/1pamA_ref2.pep
%%EXAMPLESDIR%%/seq/1pamA_ref3.pep
%%EXAMPLESDIR%%/seq/1ped_ref1.pep
%%EXAMPLESDIR%%/seq/1ped_ref2.pep
%%EXAMPLESDIR%%/seq/1ped_ref3.pep
%%EXAMPLESDIR%%/seq/1pfc_ref1.pep
%%EXAMPLESDIR%%/seq/1pfc_ref4.pep
%%EXAMPLESDIR%%/seq/1pgtA_ref1.pep
%%EXAMPLESDIR%%/seq/1pii_ref1.pep
%%EXAMPLESDIR%%/seq/1pkm_ref1.pep
%%EXAMPLESDIR%%/seq/1plc_ref1.pep
%%EXAMPLESDIR%%/seq/1ppn_ref1.pep
%%EXAMPLESDIR%%/seq/1pysA_ref1.pep
%%EXAMPLESDIR%%/seq/1qpg_ref5.pep
%%EXAMPLESDIR%%/seq/1r69.pep
%%EXAMPLESDIR%%/seq/1r69_ref1.pep
%%EXAMPLESDIR%%/seq/1r69_ref2.pep
%%EXAMPLESDIR%%/seq/1r69_ref3.pep
%%EXAMPLESDIR%%/seq/1rthA_ref1.pep
%%EXAMPLESDIR%%/seq/1sbp_ref1.pep
%%EXAMPLESDIR%%/seq/1sbp_ref2.pep
%%EXAMPLESDIR%%/seq/1sesA_ref1.pep
%%EXAMPLESDIR%%/seq/1taq_ref1.pep
%%EXAMPLESDIR%%/seq/1tgxA_ref1.pep
%%EXAMPLESDIR%%/seq/1tgxA_ref2.pep
%%EXAMPLESDIR%%/seq/1thm1_ref5.pep
%%EXAMPLESDIR%%/seq/1thm2_ref5.pep
%%EXAMPLESDIR%%/seq/1thm_ref1.pep
%%EXAMPLESDIR%%/seq/1tis_ref1.pep
%%EXAMPLESDIR%%/seq/1ton_ref1.pep
%%EXAMPLESDIR%%/seq/1tvxA_ref1.pep
%%EXAMPLESDIR%%/seq/1tvxA_ref2.pep
%%EXAMPLESDIR%%/seq/1ubi_ref1.pep
%%EXAMPLESDIR%%/seq/1ubi_ref2.pep
%%EXAMPLESDIR%%/seq/1ubi_ref3.pep
%%EXAMPLESDIR%%/seq/1uky_ref1.pep
%%EXAMPLESDIR%%/seq/1uky_ref2.pep
%%EXAMPLESDIR%%/seq/1uky_ref3.pep
%%EXAMPLESDIR%%/seq/1vln_ref4.pep
%%EXAMPLESDIR%%/seq/1wit_ref1.pep
%%EXAMPLESDIR%%/seq/1wit_ref2.pep
%%EXAMPLESDIR%%/seq/1wit_ref3.pep
%%EXAMPLESDIR%%/seq/1ycc_ref1.pep
%%EXAMPLESDIR%%/seq/1ycc_ref4.pep
%%EXAMPLESDIR%%/seq/1zin_ref1.pep
%%EXAMPLESDIR%%/seq/2ack_ref1.pep
%%EXAMPLESDIR%%/seq/2cba_ref1.pep
%%EXAMPLESDIR%%/seq/2cba_ref5.pep
%%EXAMPLESDIR%%/seq/2fxb_ref1.pep
%%EXAMPLESDIR%%/seq/2hsdA_ref1.pep
%%EXAMPLESDIR%%/seq/2hsdA_ref2.pep
%%EXAMPLESDIR%%/seq/2mhr_ref1.pep
%%EXAMPLESDIR%%/seq/2myr_ref1.pep
%%EXAMPLESDIR%%/seq/2myr_ref2.pep
%%EXAMPLESDIR%%/seq/2myr_ref3.pep
%%EXAMPLESDIR%%/seq/2pia_ref1.pep
%%EXAMPLESDIR%%/seq/2pia_ref2.pep
%%EXAMPLESDIR%%/seq/2pia_ref3.pep
%%EXAMPLESDIR%%/seq/2trx_ref1.pep
%%EXAMPLESDIR%%/seq/2trx_ref2.pep
%%EXAMPLESDIR%%/seq/3cyr_ref1.pep
%%EXAMPLESDIR%%/seq/3grs_ref1.pep
%%EXAMPLESDIR%%/seq/3grs_ref2.pep
%%EXAMPLESDIR%%/seq/3pmg_ref1.pep
%%EXAMPLESDIR%%/seq/451c_ref1.pep
%%EXAMPLESDIR%%/seq/4enl_ref1.pep
%%EXAMPLESDIR%%/seq/4enl_ref2.pep
%%EXAMPLESDIR%%/seq/4enl_ref3.pep
%%EXAMPLESDIR%%/seq/5ptp_ref1.pep
%%EXAMPLESDIR%%/seq/9rnt_ref1.pep
%%EXAMPLESDIR%%/seq/S51_ref5.pep
%%EXAMPLESDIR%%/seq/S52_ref5.pep
%%EXAMPLESDIR%%/seq/actin_ref1.pep
%%EXAMPLESDIR%%/seq/arp_ref1.pep
%%EXAMPLESDIR%%/seq/gal4_ref1.pep
%%EXAMPLESDIR%%/seq/glg_ref1.pep
%%EXAMPLESDIR%%/seq/kinase1_ref4.pep
%%EXAMPLESDIR%%/seq/kinase1_ref5.pep
%%EXAMPLESDIR%%/seq/kinase2_ref4.pep
%%EXAMPLESDIR%%/seq/kinase2_ref5.pep
%%EXAMPLESDIR%%/seq/kinase3_ref5.pep
%%EXAMPLESDIR%%/seq/kinase_ref1.pep
%%EXAMPLESDIR%%/seq/kinase_ref2.pep
%%EXAMPLESDIR%%/seq/kinase_ref3.pep
%%EXAMPLESDIR%%/test/reference_test.aln
%%EXAMPLESDIR%%/test/test.pep
%%PORTDOCS%%@dirrm %%DOCSDIR%%
@dirrm %%EXAMPLESDIR%%/seq
@dirrm %%EXAMPLESDIR%%/test
@dirrm %%EXAMPLESDIR%%

Return to bug 87264

Lines 1-3 Link Here

(-)t_coffee/Makefile (-8 / +6 lines)
		1	# ex:ts=8
1	# New ports collection makefile for: t_coffee	2	# New ports collection makefile for: t_coffee
2	# Date created: 27 June 2001	3	# Date created: 27 June 2001
3	# Whom: Johann Visagie <wjv@FreeBSD.org>	4	# Whom: Johann Visagie <wjv@FreeBSD.org>
Lines 6-12 Link Here
6	#	7	#
7		8
8	PORTNAME= t_coffee	9	PORTNAME= t_coffee
9	PORTVERSION= 2.03	10	PORTVERSION= 3.14
10	CATEGORIES= biology	11	CATEGORIES= biology
11	MASTER_SITES= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/	12	MASTER_SITES= http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
12	DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}	13	DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}
Lines 22-45 Link Here
22	CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw	23	CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
23		24
24	MAKEFILE= makefile	25	MAKEFILE= makefile
25	SCRIPTS= msf_aln2fasta_aln.pl blast_aln2fasta_aln.pl \
26	fasta_aln2fasta_aln_unique_name.pl extract_from_pdb \
27	fugue_client t_coffee_dpa t_coffee_dpa2 mocca
28		26
29	do-install:	27	do-install:
30	@ ${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin	28	@ ${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
31	.for scriptfile in ${SCRIPTS}
32	@ ${INSTALL_SCRIPT} ${WRKSRC}/bin/${scriptfile} ${PREFIX}/bin
33	.endfor
34		29
35	post-install:	30	post-install:
36	.if !defined(NOPORTDOCS)	31	.if !defined(NOPORTDOCS)
37	@ ${MKDIR} ${DOCSDIR}	32	@ ${MKDIR} ${DOCSDIR}
38	@ ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}	33	@ ${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
39	@ ${MKDIR} ${EXAMPLESDIR}	34	@ ${MKDIR} ${EXAMPLESDIR}
40	@ ${RMDIR} ${WRKSRC}/example/aln 2>/dev/null \|\| ${TRUE}
41	@ cd ${WRKSRC}/example && ${FIND} * \	35	@ cd ${WRKSRC}/example && ${FIND} * \
42	\| ${CPIO} --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}	36	\| ${CPIO} --quiet -pdum -R ${SHAREOWN}:${SHAREGRP} ${EXAMPLESDIR}
		37	@ ${MKDIR} ${DATADIR}
		38	@ ${INSTALL_DATA} ${WRKSRC}/license.txt ${DATADIR}
		39	@ ${MKDIR} ${DATADIR}/html
		40	@ ${INSTALL_DATA} ${WRKSRC}/html/* ${DATADIR}/html
43	.endif	41	.endif
44		42
45	.include <bsd.port.mk>	43	.include <bsd.port.mk>

Lines 1-161 Link Here

(-)t_coffee/pkg-plist (-156 / +54 lines)
1	bin/t_coffee	1	bin/t_coffee
2	bin/msf_aln2fasta_aln.pl
3	bin/blast_aln2fasta_aln.pl
4	bin/fasta_aln2fasta_aln_unique_name.pl
5	bin/extract_from_pdb
6	bin/fugue_client
7	bin/t_coffee_dpa
8	bin/t_coffee_dpa2
9	bin/mocca
10	%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE	2	%%PORTDOCS%%%%DOCSDIR%%/README4T-COFFEE
		3	%%PORTDOCS%%%%DOCSDIR%%/aln_compare.doc.txt
		4	%%PORTDOCS%%%%DOCSDIR%%/seq_reformat.doc.txt
11	%%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf	5	%%PORTDOCS%%%%DOCSDIR%%/t_coffee.pdf
12	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc	6	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.doc
13	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf	7	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.pdf
14	%%EXAMPLESDIR%%/seq/1aab_ref1.pep	8	%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.txt
15	%%EXAMPLESDIR%%/seq/1aboA_ref1.pep	9	%%EXAMPLESDIR%%/3d.fasta
16	%%EXAMPLESDIR%%/seq/1aboA_ref2.pep	10	%%EXAMPLESDIR%%/3d_sample2.fasta
17	%%EXAMPLESDIR%%/seq/1ac5_ref1.pep	11	%%EXAMPLESDIR%%/3d_sample3.fasta
18	%%EXAMPLESDIR%%/seq/1ad2_ref1.pep	12	%%EXAMPLESDIR%%/clustalw_method.tc_method
19	%%EXAMPLESDIR%%/seq/1ad3_ref1.pep	13	%%EXAMPLESDIR%%/command_line.txt
20	%%EXAMPLESDIR%%/seq/1adj_ref1.pep	14	%%EXAMPLESDIR%%/error_report.T-COFFEE.3752
21	%%EXAMPLESDIR%%/seq/1ag8_ref4.pep	15	%%EXAMPLESDIR%%/sample_aln1.aln
22	%%EXAMPLESDIR%%/seq/1aho_ref1.pep	16	%%EXAMPLESDIR%%/sample_aln1.fasta
23	%%EXAMPLESDIR%%/seq/1aisB_ref4.pep	17	%%EXAMPLESDIR%%/sample_aln1.tc_lib
24	%%EXAMPLESDIR%%/seq/1ajsA_ref1.pep	18	%%EXAMPLESDIR%%/sample_aln1_1.aln
25	%%EXAMPLESDIR%%/seq/1ajsA_ref2.pep	19	%%EXAMPLESDIR%%/sample_aln1_2.aln
26	%%EXAMPLESDIR%%/seq/1ajsA_ref3.pep	20	%%EXAMPLESDIR%%/sample_aln2.aln
27	%%EXAMPLESDIR%%/seq/1amk_ref1.pep	21	%%EXAMPLESDIR%%/sample_aln2.fasta
28	%%EXAMPLESDIR%%/seq/1ar1_ref4.pep	22	%%EXAMPLESDIR%%/sample_aln2.msf
29	%%EXAMPLESDIR%%/seq/1ar5A_ref1.pep	23	%%EXAMPLESDIR%%/sample_aln3.aln
30	%%EXAMPLESDIR%%/seq/1au7A_ref4.pep	24	%%EXAMPLESDIR%%/sample_aln4.aln
31	%%EXAMPLESDIR%%/seq/1aym3_ref1.pep	25	%%EXAMPLESDIR%%/sample_dnaseq1.fasta
32	%%EXAMPLESDIR%%/seq/1bbt3_ref1.pep	26	%%EXAMPLESDIR%%/struc1.pdb
33	%%EXAMPLESDIR%%/seq/1bgl_ref1.pep	27	%%EXAMPLESDIR%%/sample_lib1.mocca_lib
34	%%EXAMPLESDIR%%/seq/1ckaA_ref4.pep	28	%%EXAMPLESDIR%%/sample_lib1.tc_lib
35	%%EXAMPLESDIR%%/seq/1cpt_ref1.pep	29	%%EXAMPLESDIR%%/sample_lib2.tc_lib
36	%%EXAMPLESDIR%%/seq/1cpt_ref2.pep	30	%%EXAMPLESDIR%%/sample_lib3.tc_lib
37	%%EXAMPLESDIR%%/seq/1csp_ref1.pep	31	%%EXAMPLESDIR%%/sample_lib4.tc_lib02
38	%%EXAMPLESDIR%%/seq/1csp_ref4.pep	32	%%EXAMPLESDIR%%/sample_list1.lib_list
39	%%EXAMPLESDIR%%/seq/1csy_ref1.pep	33	%%EXAMPLESDIR%%/sample_param_file.param
40	%%EXAMPLESDIR%%/seq/1csy_ref2.pep	34	%%EXAMPLESDIR%%/sample_profile1.aln
41	%%EXAMPLESDIR%%/seq/1dlc_ref1.pep	35	%%EXAMPLESDIR%%/sample_profile2.aln
42	%%EXAMPLESDIR%%/seq/1dox_ref1.pep	36	%%EXAMPLESDIR%%/sample_seq1.aln
43	%%EXAMPLESDIR%%/seq/1eft_ref1.pep	37	%%EXAMPLESDIR%%/sample_seq1.fasta
44	%%EXAMPLESDIR%%/seq/1eft_ref5.pep	38	%%EXAMPLESDIR%%/sample_seq2.fasta
45	%%EXAMPLESDIR%%/seq/1ezm_ref1.pep	39	%%EXAMPLESDIR%%/sample_seq3.fasta
46	%%EXAMPLESDIR%%/seq/1fieA_ref1.pep	40	%%EXAMPLESDIR%%/sample_seq4.fasta
47	%%EXAMPLESDIR%%/seq/1fjlA_ref1.pep	41	%%EXAMPLESDIR%%/sample_seq5.fasta
48	%%EXAMPLESDIR%%/seq/1fkj_ref1.pep	42	%%EXAMPLESDIR%%/sample_tree.dnd
49	%%EXAMPLESDIR%%/seq/1fmb_ref1.pep	43	%%EXAMPLESDIR%%/struc2.pdb
50	%%EXAMPLESDIR%%/seq/1gdoA_ref1.pep	44	%%EXAMPLESDIR%%/struc3.pdb
51	%%EXAMPLESDIR%%/seq/1gowA_ref1.pep	45	%%EXAMPLESDIR%%/struc4.pdb
52	%%EXAMPLESDIR%%/seq/1gpb_ref1.pep	46	%%EXAMPLESDIR%%/t_coffee.log
53	%%EXAMPLESDIR%%/seq/1gtr_ref1.pep	47	%%EXAMPLESDIR%%/template_file.template
54	%%EXAMPLESDIR%%/seq/1havA_ref1.pep	48	%%EXAMPLESDIR%%/test.lib
55	%%EXAMPLESDIR%%/seq/1havA_ref2.pep	49	%%EXAMPLESDIR%%/test.tc_lib
56	%%EXAMPLESDIR%%/seq/1hfh_ref1.pep	50	%%EXAMPLESDIR%%/test_lib.tc_lib
57	%%EXAMPLESDIR%%/seq/1hpi_ref1.pep	51	%%DATADIR%%/license.txt
58	%%EXAMPLESDIR%%/seq/1idy_ref1.pep	52	%%DATADIR%%/html/t_coffee.html
59	%%EXAMPLESDIR%%/seq/1idy_ref2.pep	53	%%DATADIR%%/html/t_coffee4html.cgi
60	%%EXAMPLESDIR%%/seq/1idy_ref3.pep	54	%%PORTDOCS%% @dirrm %%DOCSDIR%%/t_coffee
61	%%EXAMPLESDIR%%/seq/1ivy_ref5.pep	55	@unexec rmdir %D/%%DOCSDIR%% 2>/dev/null \|\| true
62	%%EXAMPLESDIR%%/seq/1krn_ref1.pep	56	@dirrm %%EXAMPLESDIR%%/t_coffee
63	%%EXAMPLESDIR%%/seq/1lcf_ref1.pep	57	@unexec rmdir %D/%%EXAMPLESDIR%% 2>/dev/null \|\| true
64	%%EXAMPLESDIR%%/seq/1ldg_ref1.pep	58	@dirrm %%DATADIR%%/html
65	%%EXAMPLESDIR%%/seq/1led_ref1.pep	59	@unexec rmdir %D/%%DATADIR%% 2>/dev/null \|\| true
66	%%EXAMPLESDIR%%/seq/1lkl_ref4.pep
67	%%EXAMPLESDIR%%/seq/1lvl_ref1.pep
68	%%EXAMPLESDIR%%/seq/1lvl_ref2.pep
69	%%EXAMPLESDIR%%/seq/1mfa_ref4.pep
70	%%EXAMPLESDIR%%/seq/1mrj_ref1.pep
71	%%EXAMPLESDIR%%/seq/1pamA_ref1.pep
72	%%EXAMPLESDIR%%/seq/1pamA_ref2.pep
73	%%EXAMPLESDIR%%/seq/1pamA_ref3.pep
74	%%EXAMPLESDIR%%/seq/1ped_ref1.pep
75	%%EXAMPLESDIR%%/seq/1ped_ref2.pep
76	%%EXAMPLESDIR%%/seq/1ped_ref3.pep
77	%%EXAMPLESDIR%%/seq/1pfc_ref1.pep
78	%%EXAMPLESDIR%%/seq/1pfc_ref4.pep
79	%%EXAMPLESDIR%%/seq/1pgtA_ref1.pep
80	%%EXAMPLESDIR%%/seq/1pii_ref1.pep
81	%%EXAMPLESDIR%%/seq/1pkm_ref1.pep
82	%%EXAMPLESDIR%%/seq/1plc_ref1.pep
83	%%EXAMPLESDIR%%/seq/1ppn_ref1.pep
84	%%EXAMPLESDIR%%/seq/1pysA_ref1.pep
85	%%EXAMPLESDIR%%/seq/1qpg_ref5.pep
86	%%EXAMPLESDIR%%/seq/1r69.pep
87	%%EXAMPLESDIR%%/seq/1r69_ref1.pep
88	%%EXAMPLESDIR%%/seq/1r69_ref2.pep
89	%%EXAMPLESDIR%%/seq/1r69_ref3.pep
90	%%EXAMPLESDIR%%/seq/1rthA_ref1.pep
91	%%EXAMPLESDIR%%/seq/1sbp_ref1.pep
92	%%EXAMPLESDIR%%/seq/1sbp_ref2.pep
93	%%EXAMPLESDIR%%/seq/1sesA_ref1.pep
94	%%EXAMPLESDIR%%/seq/1taq_ref1.pep
95	%%EXAMPLESDIR%%/seq/1tgxA_ref1.pep
96	%%EXAMPLESDIR%%/seq/1tgxA_ref2.pep
97	%%EXAMPLESDIR%%/seq/1thm1_ref5.pep
98	%%EXAMPLESDIR%%/seq/1thm2_ref5.pep
99	%%EXAMPLESDIR%%/seq/1thm_ref1.pep
100	%%EXAMPLESDIR%%/seq/1tis_ref1.pep
101	%%EXAMPLESDIR%%/seq/1ton_ref1.pep
102	%%EXAMPLESDIR%%/seq/1tvxA_ref1.pep
103	%%EXAMPLESDIR%%/seq/1tvxA_ref2.pep
104	%%EXAMPLESDIR%%/seq/1ubi_ref1.pep
105	%%EXAMPLESDIR%%/seq/1ubi_ref2.pep
106	%%EXAMPLESDIR%%/seq/1ubi_ref3.pep
107	%%EXAMPLESDIR%%/seq/1uky_ref1.pep
108	%%EXAMPLESDIR%%/seq/1uky_ref2.pep
109	%%EXAMPLESDIR%%/seq/1uky_ref3.pep
110	%%EXAMPLESDIR%%/seq/1vln_ref4.pep
111	%%EXAMPLESDIR%%/seq/1wit_ref1.pep
112	%%EXAMPLESDIR%%/seq/1wit_ref2.pep
113	%%EXAMPLESDIR%%/seq/1wit_ref3.pep
114	%%EXAMPLESDIR%%/seq/1ycc_ref1.pep
115	%%EXAMPLESDIR%%/seq/1ycc_ref4.pep
116	%%EXAMPLESDIR%%/seq/1zin_ref1.pep
117	%%EXAMPLESDIR%%/seq/2ack_ref1.pep
118	%%EXAMPLESDIR%%/seq/2cba_ref1.pep
119	%%EXAMPLESDIR%%/seq/2cba_ref5.pep
120	%%EXAMPLESDIR%%/seq/2fxb_ref1.pep
121	%%EXAMPLESDIR%%/seq/2hsdA_ref1.pep
122	%%EXAMPLESDIR%%/seq/2hsdA_ref2.pep
123	%%EXAMPLESDIR%%/seq/2mhr_ref1.pep
124	%%EXAMPLESDIR%%/seq/2myr_ref1.pep
125	%%EXAMPLESDIR%%/seq/2myr_ref2.pep
126	%%EXAMPLESDIR%%/seq/2myr_ref3.pep
127	%%EXAMPLESDIR%%/seq/2pia_ref1.pep
128	%%EXAMPLESDIR%%/seq/2pia_ref2.pep
129	%%EXAMPLESDIR%%/seq/2pia_ref3.pep
130	%%EXAMPLESDIR%%/seq/2trx_ref1.pep
131	%%EXAMPLESDIR%%/seq/2trx_ref2.pep
132	%%EXAMPLESDIR%%/seq/3cyr_ref1.pep
133	%%EXAMPLESDIR%%/seq/3grs_ref1.pep
134	%%EXAMPLESDIR%%/seq/3grs_ref2.pep
135	%%EXAMPLESDIR%%/seq/3pmg_ref1.pep
136	%%EXAMPLESDIR%%/seq/451c_ref1.pep
137	%%EXAMPLESDIR%%/seq/4enl_ref1.pep
138	%%EXAMPLESDIR%%/seq/4enl_ref2.pep
139	%%EXAMPLESDIR%%/seq/4enl_ref3.pep
140	%%EXAMPLESDIR%%/seq/5ptp_ref1.pep
141	%%EXAMPLESDIR%%/seq/9rnt_ref1.pep
142	%%EXAMPLESDIR%%/seq/S51_ref5.pep
143	%%EXAMPLESDIR%%/seq/S52_ref5.pep
144	%%EXAMPLESDIR%%/seq/actin_ref1.pep
145	%%EXAMPLESDIR%%/seq/arp_ref1.pep
146	%%EXAMPLESDIR%%/seq/gal4_ref1.pep
147	%%EXAMPLESDIR%%/seq/glg_ref1.pep
148	%%EXAMPLESDIR%%/seq/kinase1_ref4.pep
149	%%EXAMPLESDIR%%/seq/kinase1_ref5.pep
150	%%EXAMPLESDIR%%/seq/kinase2_ref4.pep
151	%%EXAMPLESDIR%%/seq/kinase2_ref5.pep
152	%%EXAMPLESDIR%%/seq/kinase3_ref5.pep
153	%%EXAMPLESDIR%%/seq/kinase_ref1.pep
154	%%EXAMPLESDIR%%/seq/kinase_ref2.pep
155	%%EXAMPLESDIR%%/seq/kinase_ref3.pep
156	%%EXAMPLESDIR%%/test/reference_test.aln
157	%%EXAMPLESDIR%%/test/test.pep
158	%%PORTDOCS%%@dirrm %%DOCSDIR%%
159	@dirrm %%EXAMPLESDIR%%/seq
160	@dirrm %%EXAMPLESDIR%%/test
161	@dirrm %%EXAMPLESDIR%%