- Update to 9.03.

PR:		ports/172499
Submitted by:	KATO Tsuguru <tkato432@yahoo.com>
This commit is contained in:
Marcelo Araujo 2013-01-14 08:04:38 +00:00
parent 3b850ce68d
commit 05e78fe84a
Notes: svn2git 2021-03-31 03:12:20 +00:00
svn path=/head/; revision=310361
5 changed files with 35 additions and 219 deletions

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@ -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>

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@ -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

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@ -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

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@ -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*******************************/

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@ -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
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%%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%%