ports/87264: [maintainer update] upgrade biology/t_coffee to last version
Fernan Aguero
fernan at iib.unsam.edu.ar
Tue Oct 11 16:40:18 UTC 2005
>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 at 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 at 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 at 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 at 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%%
- at dirrm %%EXAMPLESDIR%%/seq
- at dirrm %%EXAMPLESDIR%%/test
- at 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
+ at unexec rmdir %D/%%DOCSDIR%% 2>/dev/null || true
+ at dirrm %%EXAMPLESDIR%%/t_coffee
+ at unexec rmdir %D/%%EXAMPLESDIR%% 2>/dev/null || true
+ at dirrm %%DATADIR%%/html
+ at unexec rmdir %D/%%DATADIR%% 2>/dev/null || true
--- t_coffee.diff ends here ---
>Release-Note:
>Audit-Trail:
>Unformatted:
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