Attachment 128641 Details for Bug 172499 – file.diff

[patch] file.diff

file.diff (text/plain), 14.84 KB, created by tkato432 on 2012-10-08 19:10:15 UTC

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Creator: tkato432

Created: 2012-10-08 19:10:15 UTC

Size: 14.84 KB

patch

obsolete

>diff -urN /usr/ports/biology/t_coffee/Makefile biology/t_coffee/Makefile
>--- /usr/ports/biology/t_coffee/Makefile	2012-10-01 23:45:16.000000000 +0900
>+++ biology/t_coffee/Makefile	2012-10-04 22:23:17.000000000 +0900
>@@ -2,36 +2,40 @@
> # $FreeBSD: ports/biology/t_coffee/Makefile,v 1.18 2012/10/01 14:45:16 tabthorpe Exp $
> 
> PORTNAME=	t_coffee
>-PORTVERSION=	5.68
>+PORTVERSION=	9.03
>+DISTVERSIONSUFFIX=	.r1318
> CATEGORIES=	biology
>-MASTER_SITES=	http://www.tcoffee.org/Packages/
>-DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}
>+MASTER_SITES=	http://www.tcoffee.org/Packages/Stable/%SUBDIR%/
>+MASTER_SITE_SUBDIR=	Version_${PORTVERSION}${DISTVERSIONSUFFIX}
>+DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}${DISTVERSIONSUFFIX}
> 
> MAINTAINER=	ports@FreeBSD.org
> COMMENT=	A multiple DNA or protein sequence alignment package
> 
>-BUILD_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw
>-RUN_DEPENDS:=	${BUILD_DEPENDS}
>+LICENSE=	GPLv2
>+
>+RUN_DEPENDS=	clustalw:${PORTSDIR}/biology/clustalw
>+
>+OPTIONS_DEFINE=	EXAMPLES
> 
> BUILD_WRKSRC=	${WRKSRC}/t_coffee_source
>-MAKE_ENV=	MV=${MV} USER_BIN=${PREFIX}/bin \
>-		CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
> 
>+USE_FORTRAN=	yes
>+MAKE_ENV=	FCC="${FC} ${FFLAGS}"
> MAKEFILE=	makefile
>+MAKE_JOBS_SAFE=	yes
> 
>-do-install:
>-	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
>+PORTEXAMPLES=	*
>+PLIST_FILES=	bin/TMalign bin/t_coffee
> 
>-post-install:
>-.if !defined(NOPORTDOCS)
>-	@ ${MKDIR} ${DOCSDIR}/html
>-	${INSTALL_DATA} ${WRKSRC}/doc/* ${DOCSDIR}
>-	${INSTALL_DATA} ${WRKSRC}/license.txt ${DOCSDIR}
>-	${INSTALL_DATA} ${WRKSRC}/html/* ${DOCSDIR}/html
>-.endif
>-.if !defined(NOPORTEXAMPLES)
>-	@ ${MKDIR} ${EXAMPLESDIR}
>-	cd ${WRKSRC}/example && ${COPYTREE_SHARE} \* ${EXAMPLESDIR}
>+.include <bsd.port.options.mk>
>+
>+do-install:
>+	(cd ${BUILD_WRKSRC} \
>+		&& ${INSTALL_PROGRAM} TMalign t_coffee ${PREFIX}/bin)
>+.if ${PORT_OPTIONS:MEXAMPLES}
>+	@${MKDIR} ${EXAMPLESDIR}
>+	@(cd ${WRKSRC}/example && ${COPYTREE_SHARE} . ${EXAMPLESDIR})
> .endif
> 
> .include <bsd.port.mk>
>diff -urN /usr/ports/biology/t_coffee/distinfo biology/t_coffee/distinfo
>--- /usr/ports/biology/t_coffee/distinfo	2011-03-19 21:29:38.000000000 +0900
>+++ biology/t_coffee/distinfo	2012-10-04 22:02:57.000000000 +0900
>@@ -1,2 +1,2 @@
>-SHA256 (T-COFFEE_distribution_Version_5.68.tar.gz) = 137d188cef6f33a42cbd656482eb961d1588fef3091d2457ee0ef23fab16a6de
>-SIZE (T-COFFEE_distribution_Version_5.68.tar.gz) = 2875438
>+SHA256 (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 5bb9a531a4036b741a8ff0fe19f3591a3f33bf7ac4f484e5329b1b5dd1fff43c
>+SIZE (T-COFFEE_distribution_Version_9.03.r1318.tar.gz) = 3455629
>diff -urN /usr/ports/biology/t_coffee/files/patch-Makefile biology/t_coffee/files/patch-Makefile
>--- /usr/ports/biology/t_coffee/files/patch-Makefile	2006-02-10 18:45:28.000000000 +0900
>+++ biology/t_coffee/files/patch-Makefile	1970-01-01 09:00:00.000000000 +0900
>@@ -1,8 +0,0 @@
>---- t_coffee_source/makefile.orig	Tue Feb  7 15:11:00 2006
>-+++ t_coffee_source/makefile	Tue Feb  7 15:10:36 2006
>-@@ -1,4 +1,4 @@
>--CC=cc
>-+#CC=cc
>- 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 
>- 	$(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
>- 	mv  t_coffee  ../bin
>diff -urN /usr/ports/biology/t_coffee/files/patch-dev3.c biology/t_coffee/files/patch-dev3.c
>--- /usr/ports/biology/t_coffee/files/patch-dev3.c	1970-01-01 09:00:00.000000000 +0900
>+++ biology/t_coffee/files/patch-dev3.c	2012-10-04 22:14:42.000000000 +0900
>@@ -0,0 +1,10 @@
>+--- t_coffee_source/dev3.c.orig	2012-07-13 02:06:31.000000000 +0900
>++++ t_coffee_source/dev3.c	2012-10-04 22:14:10.000000000 +0900
>+@@ -3,6 +3,7 @@
>+ #include <math.h>
>+ #include <stdarg.h>
>+ #include <string.h>
>++#include <sys/types.h>
>+ #include <sys/sysctl.h>
>+ #include "dev3_lib_header.h"
>+ /******************************COPYRIGHT NOTICE*******************************/
>diff -urN /usr/ports/biology/t_coffee/pkg-plist biology/t_coffee/pkg-plist
>--- /usr/ports/biology/t_coffee/pkg-plist	2008-09-09 22:43:15.000000000 +0900
>+++ biology/t_coffee/pkg-plist	1970-01-01 09:00:00.000000000 +0900
>@@ -1,190 +0,0 @@
>-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%%

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Attachments on bug 172499: 128641