- Update to 9.03.

PR:		ports/172499
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>

5 files changed, 35 insertions, 219 deletions

diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
index 216884fc8d47..6e6c28d7b721 100644
--- a/biology/t_coffee/Makefile
+++ b/biology/t_coffee/Makefile
@@ -2,36 +2,40 @@
 # $FreeBSD$
 
 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
+
+PORTEXAMPLES=	*
+PLIST_FILES=	bin/TMalign bin/t_coffee
+
+.include <bsd.port.options.mk>
 
 do-install:
-	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
-
-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}
+	(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 --git a/biology/t_coffee/distinfo b/biology/t_coffee/distinfo
index 26866a9cae0d..376d92c9077b 100644
--- a/biology/t_coffee/distinfo
+++ b/biology/t_coffee/distinfo
@@ -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 --git a/biology/t_coffee/files/patch-Makefile b/biology/t_coffee/files/patch-Makefile
deleted file mode 100644
index 5cf4496b912f..000000000000
--- a/biology/t_coffee/files/patch-Makefile
+++ /dev/null
@@ -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 --git a/biology/t_coffee/files/patch-dev3.c b/biology/t_coffee/files/patch-dev3.c
new file mode 100644
index 000000000000..0b1335e5c5d9
--- /dev/null
+++ b/biology/t_coffee/files/patch-dev3.c
@@ -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 --git a/biology/t_coffee/pkg-plist b/biology/t_coffee/pkg-plist
deleted file mode 100644
index 21736fc61d28..000000000000
--- a/biology/t_coffee/pkg-plist
+++ /dev/null
@@ -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%%