Attachment 86062 Details for Bug 122435 – file.diff

[patch] file.diff

file.diff (text/plain), 3.74 KB, created by Fernan Aguero on 2008-04-04 05:50:01 UTC

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Creator: Fernan Aguero

Created: 2008-04-04 05:50:01 UTC

Size: 3.74 KB

patch

obsolete

>diff -ruN --exclude CVS /usr/ports/biology/t_coffee/Makefile t_coffee/Makefile
>--- /usr/ports/biology/t_coffee/Makefile	Fri May 18 10:22:28 2007
>+++ t_coffee/Makefile	Wed Apr  2 18:12:58 2008
>@@ -7,7 +7,7 @@
> #
> 
> PORTNAME=	t_coffee
>-PORTVERSION=	4.96
>+PORTVERSION=	5.68
> CATEGORIES=	biology
> MASTER_SITES=	http://www.tcoffee.org/Packages/
> DISTNAME=	T-COFFEE_distribution_Version_${PORTVERSION}
>@@ -23,7 +23,6 @@
> 		CLUSTALW_4_TCOFFEE=${LOCALBASE}/bin/clustalw
> 
> MAKEFILE=	makefile
>-USE_GCC=	3.3
> 
> do-install:
> 	${INSTALL_PROGRAM} ${WRKSRC}/bin/t_coffee ${PREFIX}/bin
>diff -ruN --exclude CVS /usr/ports/biology/t_coffee/distinfo t_coffee/distinfo
>--- /usr/ports/biology/t_coffee/distinfo	Sat Mar 10 18:08:13 2007
>+++ t_coffee/distinfo	Wed Apr  2 17:49:10 2008
>@@ -1,3 +1,3 @@
>-MD5 (T-COFFEE_distribution_Version_4.96.tar.gz) = ce40b2654663b7c22c1c8427fb5e32db
>-SHA256 (T-COFFEE_distribution_Version_4.96.tar.gz) = 49181acd69a5723fd5b11f579b1efe685b5289bf187985b25b40c514b0af0213
>-SIZE (T-COFFEE_distribution_Version_4.96.tar.gz) = 2863327
>+MD5 (T-COFFEE_distribution_Version_5.68.tar.gz) = 77316ccd4790c3c6e1b118681e15c10e
>+SHA256 (T-COFFEE_distribution_Version_5.68.tar.gz) = 137d188cef6f33a42cbd656482eb961d1588fef3091d2457ee0ef23fab16a6de
>+SIZE (T-COFFEE_distribution_Version_5.68.tar.gz) = 2875438
>diff -ruN --exclude CVS /usr/ports/biology/t_coffee/pkg-plist t_coffee/pkg-plist
>--- /usr/ports/biology/t_coffee/pkg-plist	Sat Mar 10 18:08:13 2007
>+++ t_coffee/pkg-plist	Wed Apr  2 18:11:58 2008
>@@ -2,7 +2,6 @@
> %%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_technical.doc
> %%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm
> %%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt
>@@ -33,6 +32,7 @@
> %%EXAMPLESDIR%%/g10.aln
> %%EXAMPLESDIR%%/g15.aln
> %%EXAMPLESDIR%%/g5.aln
>+%%EXAMPLESDIR%%/kinases.aln
> %%EXAMPLESDIR%%/marna.tc_lib
> %%EXAMPLESDIR%%/new_profile1_pdb1.aln
> %%EXAMPLESDIR%%/new_profile1_pdb1.html
>@@ -52,6 +52,7 @@
> %%EXAMPLESDIR%%/profile1_pdb1.aln
> %%EXAMPLESDIR%%/profile1_pdb1.fasta
> %%EXAMPLESDIR%%/profile1_pdb1.html
>+%%EXAMPLESDIR%%/seq.fas
> %%EXAMPLESDIR%%/profile1_pdb1_1.aln
> %%EXAMPLESDIR%%/profile1_pdb1_1.html
> %%EXAMPLESDIR%%/profile2_pdb2.aln
>@@ -86,10 +87,11 @@
> %%EXAMPLESDIR%%/sample_param_file.param
> %%EXAMPLESDIR%%/sample_profile1.aln
> %%EXAMPLESDIR%%/sample_profile2.aln
>+%%EXAMPLESDIR%%/sample_rnaseq1.fasta
> %%EXAMPLESDIR%%/sample_seq1.aln
>+%%EXAMPLESDIR%%/sv.aln
> %%EXAMPLESDIR%%/sample_seq1.fasta
> %%EXAMPLESDIR%%/sample_seq2.fasta
>-%%EXAMPLESDIR%%/seq.fas
> %%EXAMPLESDIR%%/sample_seq3.fasta
> %%EXAMPLESDIR%%/sample_seq4.fasta
> %%EXAMPLESDIR%%/sample_seq5.fasta
>@@ -133,13 +135,12 @@
> %%EXAMPLESDIR%%/sproteases_small.g10.html
> %%EXAMPLESDIR%%/sproteases_small.g10.score_ascii
> %%EXAMPLESDIR%%/sproteases_small.g15.cw_aln
>+%%EXAMPLESDIR%%/sproteases_small.ph
> %%EXAMPLESDIR%%/sproteases_small.g15.html
> %%EXAMPLESDIR%%/sproteases_small.html
>-%%EXAMPLESDIR%%/struc1.pdb
> %%EXAMPLESDIR%%/sproteases_small.mafft
> %%EXAMPLESDIR%%/sproteases_small.mcoffee
> %%EXAMPLESDIR%%/sproteases_small.muscle
>-%%EXAMPLESDIR%%/sproteases_small.ph
> %%EXAMPLESDIR%%/sproteases_small.probcons
> %%EXAMPLESDIR%%/sproteases_small.score_ascii
> %%EXAMPLESDIR%%/sproteases_small.score_html
>@@ -148,6 +149,7 @@
> %%EXAMPLESDIR%%/sproteases_small.tc_aln.html
> %%EXAMPLESDIR%%/sproteases_small.template_file
> %%EXAMPLESDIR%%/sproteases_small_dna.fasta
>+%%EXAMPLESDIR%%/struc1.pdb
> %%EXAMPLESDIR%%/struc2.pdb
> %%EXAMPLESDIR%%/struc3.pdb
> %%EXAMPLESDIR%%/struc4.pdb
>@@ -155,7 +157,6 @@
> %%EXAMPLESDIR%%/struc6.pdb
> %%EXAMPLESDIR%%/struc7.pdb
> %%EXAMPLESDIR%%/struc8.pdb
>-%%EXAMPLESDIR%%/sv.aln
> %%EXAMPLESDIR%%/sv.dnd
> %%EXAMPLESDIR%%/sv.fasta
> %%EXAMPLESDIR%%/sv.html

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Attachments on bug 122435: 86062