Attachment 57856 Details for Bug 87264 – t_coffee.diff

[patch] t_coffee.diff

t_coffee.diff (text/plain), 9.91 KB, created by Fernan Aguero on 2005-10-11 17:40:16 UTC

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Creator: Fernan Aguero

Created: 2005-10-11 17:40:16 UTC

Size: 9.91 KB

patch

obsolete

>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

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Attachments on bug 87264: 57856