diff options
Diffstat (limited to 'biology')
| -rw-r--r-- | biology/t_coffee/Makefile | 42 | ||||
| -rw-r--r-- | biology/t_coffee/distinfo | 4 | ||||
| -rw-r--r-- | biology/t_coffee/files/patch-Makefile | 8 | ||||
| -rw-r--r-- | biology/t_coffee/files/patch-dev3.c | 10 | ||||
| -rw-r--r-- | biology/t_coffee/pkg-plist | 190 |
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%% |