4 files changed, 61 insertions, 167 deletions

diff --git a/biology/t_coffee/Makefile b/biology/t_coffee/Makefile
index 86b1078ecbbc..98fbf028f3ee 100644
--- a/biology/t_coffee/Makefile
+++ b/biology/t_coffee/Makefile
@@ -1,3 +1,4 @@
+# ex:ts=8
 # New ports collection makefile for:	t_coffee
 # Date created:		27 June 2001
 # Whom:	      		Johann Visagie <wjv@FreeBSD.org>
@@ -6,7 +7,7 @@
 #
 
 PORTNAME=	t_coffee
-PORTVERSION=	2.03
+PORTVERSION=	3.14
 CATEGORIES=	biology
 MASTER_SITES=	http://igs-server.cnrs-mrs.fr/~cnotred/Packages/
 DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}
@@ -22,24 +23,21 @@ MAKE_ENV=	MV=${MV} USER_BIN=${PREFIX}/bin \
 		CLUSTALW_4_TCOFFEE=${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>
diff --git a/biology/t_coffee/distinfo b/biology/t_coffee/distinfo
index 5589c4f91de5..0fcb658a6e53 100644
--- a/biology/t_coffee/distinfo
+++ b/biology/t_coffee/distinfo
@@ -1,2 +1,2 @@
-MD5 (T-COFFEE_distribution_Version_2.03.tar.gz) = a86e2d83c17058b03be0170566d634f0
-SIZE (T-COFFEE_distribution_Version_2.03.tar.gz) = 864853
+MD5 (T-COFFEE_distribution_Version_3.14.tar.gz) = ad467933434fbe7137b08aea30a79922
+SIZE (T-COFFEE_distribution_Version_3.14.tar.gz) = 1533171
diff --git a/biology/t_coffee/pkg-descr b/biology/t_coffee/pkg-descr
index ff1051aeb958..e0490fb5f39b 100644
--- a/biology/t_coffee/pkg-descr
+++ b/biology/t_coffee/pkg-descr
@@ -16,6 +16,6 @@ From the website:
     407-422,1998
 
 Author: Cedric Notredame <cedric.notredame@europe.com>
-WWW:    http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
+WWW: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
 
 -- Johann Visagie <wjv@FreeBSD.org>
diff --git a/biology/t_coffee/pkg-plist b/biology/t_coffee/pkg-plist
index d719ed2fdec2..a60991b5f435 100644
--- a/biology/t_coffee/pkg-plist
+++ b/biology/t_coffee/pkg-plist
@@ -1,161 +1,57 @@
 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
-%%EXAMPLESDIR%%/seq/1aab_ref1.pep
-%%EXAMPLESDIR%%/seq/1aboA_ref1.pep
-%%EXAMPLESDIR%%/seq/1aboA_ref2.pep
-%%EXAMPLESDIR%%/seq/1ac5_ref1.pep
-%%EXAMPLESDIR%%/seq/1ad2_ref1.pep
-%%EXAMPLESDIR%%/seq/1ad3_ref1.pep
-%%EXAMPLESDIR%%/seq/1adj_ref1.pep
-%%EXAMPLESDIR%%/seq/1ag8_ref4.pep
-%%EXAMPLESDIR%%/seq/1aho_ref1.pep
-%%EXAMPLESDIR%%/seq/1aisB_ref4.pep
-%%EXAMPLESDIR%%/seq/1ajsA_ref1.pep
-%%EXAMPLESDIR%%/seq/1ajsA_ref2.pep
-%%EXAMPLESDIR%%/seq/1ajsA_ref3.pep
-%%EXAMPLESDIR%%/seq/1amk_ref1.pep
-%%EXAMPLESDIR%%/seq/1ar1_ref4.pep
-%%EXAMPLESDIR%%/seq/1ar5A_ref1.pep
-%%EXAMPLESDIR%%/seq/1au7A_ref4.pep
-%%EXAMPLESDIR%%/seq/1aym3_ref1.pep
-%%EXAMPLESDIR%%/seq/1bbt3_ref1.pep
-%%EXAMPLESDIR%%/seq/1bgl_ref1.pep
-%%EXAMPLESDIR%%/seq/1ckaA_ref4.pep
-%%EXAMPLESDIR%%/seq/1cpt_ref1.pep
-%%EXAMPLESDIR%%/seq/1cpt_ref2.pep
-%%EXAMPLESDIR%%/seq/1csp_ref1.pep
-%%EXAMPLESDIR%%/seq/1csp_ref4.pep
-%%EXAMPLESDIR%%/seq/1csy_ref1.pep
-%%EXAMPLESDIR%%/seq/1csy_ref2.pep
-%%EXAMPLESDIR%%/seq/1dlc_ref1.pep
-%%EXAMPLESDIR%%/seq/1dox_ref1.pep
-%%EXAMPLESDIR%%/seq/1eft_ref1.pep
-%%EXAMPLESDIR%%/seq/1eft_ref5.pep
-%%EXAMPLESDIR%%/seq/1ezm_ref1.pep
-%%EXAMPLESDIR%%/seq/1fieA_ref1.pep
-%%EXAMPLESDIR%%/seq/1fjlA_ref1.pep
-%%EXAMPLESDIR%%/seq/1fkj_ref1.pep
-%%EXAMPLESDIR%%/seq/1fmb_ref1.pep
-%%EXAMPLESDIR%%/seq/1gdoA_ref1.pep
-%%EXAMPLESDIR%%/seq/1gowA_ref1.pep
-%%EXAMPLESDIR%%/seq/1gpb_ref1.pep
-%%EXAMPLESDIR%%/seq/1gtr_ref1.pep
-%%EXAMPLESDIR%%/seq/1havA_ref1.pep
-%%EXAMPLESDIR%%/seq/1havA_ref2.pep
-%%EXAMPLESDIR%%/seq/1hfh_ref1.pep
-%%EXAMPLESDIR%%/seq/1hpi_ref1.pep
-%%EXAMPLESDIR%%/seq/1idy_ref1.pep
-%%EXAMPLESDIR%%/seq/1idy_ref2.pep
-%%EXAMPLESDIR%%/seq/1idy_ref3.pep
-%%EXAMPLESDIR%%/seq/1ivy_ref5.pep
-%%EXAMPLESDIR%%/seq/1krn_ref1.pep
-%%EXAMPLESDIR%%/seq/1lcf_ref1.pep
-%%EXAMPLESDIR%%/seq/1ldg_ref1.pep
-%%EXAMPLESDIR%%/seq/1led_ref1.pep
-%%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%%
+%%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
+@unexec rmdir %D/%%DOCSDIR%% 2>/dev/null || true
+@unexec rmdir %D/%%EXAMPLESDIR%% 2>/dev/null || true
+@dirrm %%DATADIR%%/html
+@unexec rmdir %D/%%DATADIR%% 2>/dev/null || true