ports/122435: [maintainer] update tcoffee to latest version

[Fernan Aguero]

>Number:         122435
>Category:       ports
>Synopsis:       [maintainer] update tcoffee to latest version
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          maintainer-update
>Submitter-Id:   current-users
>Arrival-Date:   Fri Apr 04 04:50:01 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator:     Fernan Aguero
>Release:        6.3
>Organization:
IIB-UNSAM
>Environment:
>Description:

>How-To-Repeat:

>Fix:


Patch attached with submission follows:

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


>Release-Note:
>Audit-Trail:
>Unformatted: