Date: Tue, 11 Oct 2005 13:39:25 -0300 (ART) From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/87264: [maintainer update] upgrade biology/t_coffee to last version Message-ID: <200510111639.j9BGdPWA032778@pi.iib.unsam.edu.ar> Resent-Message-ID: <200510111640.j9BGeGud022819@freefall.freebsd.org>
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>Number: 87264 >Category: ports >Synopsis: [maintainer update] upgrade biology/t_coffee to last version >Confidential: no >Severity: serious >Priority: medium >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: maintainer-update >Submitter-Id: current-users >Arrival-Date: Tue Oct 11 16:40:16 GMT 2005 >Closed-Date: >Last-Modified: >Originator: Fernan Aguero >Release: FreeBSD 4.10-RELEASE i386 >Organization: IIB-UNSAM >Environment: FreeBSD pi.iib.unsam.edu.ar 4.10-RELEASE FreeBSD 4.10-RELEASE #0: Wed May 26 12:56:43 ART 2004 fernan@pi.iib.unsam.edu.ar:/usr/obj/usr/src/sys/PI i386 >Description: Upgrade t_coffee to last version. This fixes the problems noticed by Bill Fenner's port survey (fetching of distfile impossible due to retirement of old version). >How-To-Repeat: >Fix: --- t_coffee.diff begins here --- diff -ruN /usr/ports/biology/t_coffee/Makefile t_coffee/Makefile --- /usr/ports/biology/t_coffee/Makefile Mon Nov 29 06:06:34 2004 +++ t_coffee/Makefile Fri Oct 7 06:54:54 2005 @@ -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_${PORTVERSION} @@ -22,24 +23,21 @@ CLUSTALW_4_TCOFFEE=${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 -ruN /usr/ports/biology/t_coffee/distinfo t_coffee/distinfo --- /usr/ports/biology/t_coffee/distinfo Mon Nov 29 06:06:34 2004 +++ t_coffee/distinfo Fri Oct 7 06:31:06 2005 @@ -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 -ruN /usr/ports/biology/t_coffee/pkg-descr t_coffee/pkg-descr --- /usr/ports/biology/t_coffee/pkg-descr Mon Nov 29 06:06:34 2004 +++ t_coffee/pkg-descr Fri Oct 7 06:56:32 2005 @@ -16,6 +16,6 @@ 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 -ruN /usr/ports/biology/t_coffee/pkg-plist t_coffee/pkg-plist --- /usr/ports/biology/t_coffee/pkg-plist Mon Nov 29 06:06:34 2004 +++ t_coffee/pkg-plist Fri Oct 7 08:51:08 2005 @@ -1,161 +1,59 @@ 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 +%%PORTDOCS%% @dirrm %%DOCSDIR%%/t_coffee +@unexec rmdir %D/%%DOCSDIR%% 2>/dev/null || true +@dirrm %%EXAMPLESDIR%%/t_coffee +@unexec rmdir %D/%%EXAMPLESDIR%% 2>/dev/null || true +@dirrm %%DATADIR%%/html +@unexec rmdir %D/%%DATADIR%% 2>/dev/null || true --- t_coffee.diff ends here --- >Release-Note: >Audit-Trail: >Unformatted:
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