Date: Fri, 4 Apr 2008 04:48:10 GMT From: Fernan Aguero <fernan@iib.unsam.edu.ar> To: freebsd-gnats-submit@FreeBSD.org Subject: ports/122435: [maintainer] update tcoffee to latest version Message-ID: <200804040448.m344mATF093497@www.freebsd.org> Resent-Message-ID: <200804040450.m344o1Yx076436@freefall.freebsd.org>
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>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:
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