ports/110080: [maintainer] update tcoffee to latest version
Fernan Aguero
fernan at iib.unsam.edu.ar
Thu Mar 8 12:20:04 UTC 2007
>Number: 110080
>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: Thu Mar 08 12:20:04 GMT 2007
>Closed-Date:
>Last-Modified:
>Originator: Fernan Aguero
>Release: FreeBSD-6.2
>Organization:
IIB-UNSAM
>Environment:
>Description:
update tcoffee to latest version
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
diff --exclude CVS -ruN /usr/ports/biology/t_coffee/Makefile t_coffee/Makefile
--- /usr/ports/biology/t_coffee/Makefile Tue Feb 6 16:23:53 2007
+++ t_coffee/Makefile Wed Mar 7 15:19:12 2007
@@ -7,7 +7,7 @@
#
PORTNAME= t_coffee
-PORTVERSION= 3.27
+PORTVERSION= 4.96
CATEGORIES= biology
MASTER_SITES= http://www.tcoffee.org/Packages/
DISTNAME= T-COFFEE_distribution_Version_${PORTVERSION}
diff --exclude CVS -ruN /usr/ports/biology/t_coffee/distinfo t_coffee/distinfo
--- /usr/ports/biology/t_coffee/distinfo Fri Feb 10 06:45:28 2006
+++ t_coffee/distinfo Wed Mar 7 15:11:20 2007
@@ -1,3 +1,3 @@
-MD5 (T-COFFEE_distribution_Version_3.27.tar.gz) = 747d907f4b87e07d7b1e670a2b263e23
-SHA256 (T-COFFEE_distribution_Version_3.27.tar.gz) = ffb7920919b24a6144492bec71580cda8a3ef4698acf762f76ebadfcae9aa01a
-SIZE (T-COFFEE_distribution_Version_3.27.tar.gz) = 1295287
+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
diff --exclude CVS -ruN /usr/ports/biology/t_coffee/pkg-plist t_coffee/pkg-plist
--- /usr/ports/biology/t_coffee/pkg-plist Sat Jan 21 22:25:24 2006
+++ t_coffee/pkg-plist Wed Mar 7 15:15:18 2007
@@ -3,16 +3,63 @@
%%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
-%%PORTDOCS%%%%DOCSDIR%%/t_coffee_doc.txt
+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.doc
+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.htm
+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_technical.txt
+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.doc
+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.htm
+%%PORTDOCS%%%%DOCSDIR%%/t_coffee_tutorial.txt
+%%EXAMPLESDIR%%/2seqs.fas
+%%EXAMPLESDIR%%/3d.aln
+%%EXAMPLESDIR%%/3d.dnd
%%EXAMPLESDIR%%/3d.fasta
+%%EXAMPLESDIR%%/3d.html
%%EXAMPLESDIR%%/3d_sample2.fasta
%%EXAMPLESDIR%%/3d_sample3.fasta
+%%EXAMPLESDIR%%/3d_sample4.aln
+%%EXAMPLESDIR%%/b30.aln
+%%EXAMPLESDIR%%/block1.aln
+%%EXAMPLESDIR%%/block2.aln
+%%EXAMPLESDIR%%/cache
+%%EXAMPLESDIR%%/charge_relay_lib.tc_lib
%%EXAMPLESDIR%%/clustalw_method.tc_method
+%%EXAMPLESDIR%%/combined_aln.aln
+%%EXAMPLESDIR%%/combined_aln.aln.aln
+%%EXAMPLESDIR%%/combined_aln.aln.html
%%EXAMPLESDIR%%/command_line.txt
-%%EXAMPLESDIR%%/error_report.T-COFFEE.3752
+%%EXAMPLESDIR%%/error_report.T-COFFEE
+%%EXAMPLESDIR%%/g0.aln
+%%EXAMPLESDIR%%/x
+%%EXAMPLESDIR%%/g10.aln
+%%EXAMPLESDIR%%/g15.aln
+%%EXAMPLESDIR%%/g5.aln
+%%EXAMPLESDIR%%/marna.tc_lib
+%%EXAMPLESDIR%%/new_profile1_pdb1.aln
+%%EXAMPLESDIR%%/new_profile1_pdb1.html
+%%EXAMPLESDIR%%/newprf.aln
+%%EXAMPLESDIR%%/newprf.html
+%%EXAMPLESDIR%%/p120.aln
+%%EXAMPLESDIR%%/p250
+%%EXAMPLESDIR%%/p350.aln
+%%EXAMPLESDIR%%/prf1.aln
+%%EXAMPLESDIR%%/prf1.dnd
+%%EXAMPLESDIR%%/prf1.fasta
+%%EXAMPLESDIR%%/prf2.aln
+%%EXAMPLESDIR%%/prf2.dnd
+%%EXAMPLESDIR%%/prf2.fasta
+%%EXAMPLESDIR%%/prf3.aln
+%%EXAMPLESDIR%%/prf3.fasta
+%%EXAMPLESDIR%%/profile1_pdb1.aln
+%%EXAMPLESDIR%%/profile1_pdb1.fasta
+%%EXAMPLESDIR%%/profile1_pdb1.html
+%%EXAMPLESDIR%%/profile1_pdb1_1.aln
+%%EXAMPLESDIR%%/profile1_pdb1_1.html
+%%EXAMPLESDIR%%/profile2_pdb2.aln
+%%EXAMPLESDIR%%/profile2_pdb2.dnd
+%%EXAMPLESDIR%%/profile2_pdb2.fasta
+%%EXAMPLESDIR%%/profile2_pdb2.html
%%EXAMPLESDIR%%/sample_aln1.aln
+%%EXAMPLESDIR%%/sample_aln1.dnd
%%EXAMPLESDIR%%/sample_aln1.fasta
%%EXAMPLESDIR%%/sample_aln1.tc_lib
%%EXAMPLESDIR%%/sample_aln1_1.aln
@@ -22,13 +69,19 @@
%%EXAMPLESDIR%%/sample_aln2.msf
%%EXAMPLESDIR%%/sample_aln3.aln
%%EXAMPLESDIR%%/sample_aln4.aln
+%%EXAMPLESDIR%%/sample_aln5.aln
+%%EXAMPLESDIR%%/sample_aln6.aln
+%%EXAMPLESDIR%%/sample_aln6.cache
+%%EXAMPLESDIR%%/sample_aln6.html
+%%EXAMPLESDIR%%/sample_aln7.aln
+%%EXAMPLESDIR%%/sample_aln7.cache_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_lib5.tc_lib
%%EXAMPLESDIR%%/sample_list1.lib_list
%%EXAMPLESDIR%%/sample_param_file.param
%%EXAMPLESDIR%%/sample_profile1.aln
@@ -36,22 +89,102 @@
%%EXAMPLESDIR%%/sample_seq1.aln
%%EXAMPLESDIR%%/sample_seq1.fasta
%%EXAMPLESDIR%%/sample_seq2.fasta
+%%EXAMPLESDIR%%/seq.fas
%%EXAMPLESDIR%%/sample_seq3.fasta
%%EXAMPLESDIR%%/sample_seq4.fasta
%%EXAMPLESDIR%%/sample_seq5.fasta
+%%EXAMPLESDIR%%/sample_seq6.fasta
+%%EXAMPLESDIR%%/sample_seq7.fasta
+%%EXAMPLESDIR%%/sample_seq8.seq
%%EXAMPLESDIR%%/sample_tree.dnd
+%%EXAMPLESDIR%%/sample_tree2.dnd
+%%EXAMPLESDIR%%/sample_tree3.dnd
+%%EXAMPLESDIR%%/sproteases.small
+%%EXAMPLESDIR%%/sproteases.small.blosum62mt.sim_file
+%%EXAMPLESDIR%%/sproteases1_small.aln
+%%EXAMPLESDIR%%/sproteases1_small.dnd
+%%EXAMPLESDIR%%/sproteases1_small.fasta
+%%EXAMPLESDIR%%/sproteases2_small.aln
+%%EXAMPLESDIR%%/sproteases2_small.dnd
+%%EXAMPLESDIR%%/sproteases2_small.fasta
+%%EXAMPLESDIR%%/sproteases_chain.fasta
+%%EXAMPLESDIR%%/sproteases_large.aln
+%%EXAMPLESDIR%%/sproteases_large.code_name
+%%EXAMPLESDIR%%/sproteases_large.coded.fasta
+%%EXAMPLESDIR%%/sproteases_large.dnd
+%%EXAMPLESDIR%%/sproteases_large.fasta
+%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim2_file
+%%EXAMPLESDIR%%/sproteases_large.fasta.blosum62mt.sim_file
+%%EXAMPLESDIR%%/sproteases_large.fasta~
+%%EXAMPLESDIR%%/sproteases_large.html
+%%EXAMPLESDIR%%/sproteases_large.muscle
+%%EXAMPLESDIR%%/sproteases_large_muscle_trim.aln
+%%EXAMPLESDIR%%/sproteases_oneseq.fasta
+%%EXAMPLESDIR%%/sproteases_pair.fasta
+%%EXAMPLESDIR%%/sproteases_small.aln
+%%EXAMPLESDIR%%/sproteases_small.b62_aln
+%%EXAMPLESDIR%%/sproteases_small.cw_aln
+%%EXAMPLESDIR%%/sproteases_small.dnd
+%%EXAMPLESDIR%%/sproteases_small.expresso
+%%EXAMPLESDIR%%/sproteases_small.fasta
+%%EXAMPLESDIR%%/sproteases_small.g0.aln
+%%EXAMPLESDIR%%/sproteases_small.g0.cw_aln
+%%EXAMPLESDIR%%/sproteases_small.g10.cw_aln
+%%EXAMPLESDIR%%/sproteases_small.g10.html
+%%EXAMPLESDIR%%/sproteases_small.g10.score_ascii
+%%EXAMPLESDIR%%/sproteases_small.g15.cw_aln
+%%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
+%%EXAMPLESDIR%%/sproteases_small.tc_aln
+%%EXAMPLESDIR%%/sproteases_small.tc_aln.aln
+%%EXAMPLESDIR%%/sproteases_small.tc_aln.html
+%%EXAMPLESDIR%%/sproteases_small.template_file
+%%EXAMPLESDIR%%/sproteases_small_dna.fasta
%%EXAMPLESDIR%%/struc2.pdb
%%EXAMPLESDIR%%/struc3.pdb
%%EXAMPLESDIR%%/struc4.pdb
+%%EXAMPLESDIR%%/struc5.pdb
+%%EXAMPLESDIR%%/struc6.pdb
+%%EXAMPLESDIR%%/struc7.pdb
+%%EXAMPLESDIR%%/struc8.pdb
+%%EXAMPLESDIR%%/sv.aln
+%%EXAMPLESDIR%%/sv.dnd
+%%EXAMPLESDIR%%/sv.fasta
+%%EXAMPLESDIR%%/sv.html
+%%EXAMPLESDIR%%/sv.maln
%%EXAMPLESDIR%%/t_coffee.log
%%EXAMPLESDIR%%/template_file.template
+%%EXAMPLESDIR%%/template_file6.template
+%%EXAMPLESDIR%%/template_file7.template
%%EXAMPLESDIR%%/test.lib
%%EXAMPLESDIR%%/test.tc_lib
%%EXAMPLESDIR%%/test_lib.tc_lib
+%%EXAMPLESDIR%%/three_pdb.aln
+%%EXAMPLESDIR%%/three_pdb.dnd
+%%EXAMPLESDIR%%/three_pdb.fasta
+%%EXAMPLESDIR%%/three_pdb_two_seq.aln
+%%EXAMPLESDIR%%/three_pdb_two_seq.dnd
+%%EXAMPLESDIR%%/three_pdb_two_seq.fasta
+%%EXAMPLESDIR%%/three_pdb_two_seq.fasta~
+%%EXAMPLESDIR%%/tlara_libraries.tar
+%%EXAMPLESDIR%%/tlara_tRNA_aln10.output
+%%EXAMPLESDIR%%/tlara_tRNA_aln50.output
+%%EXAMPLESDIR%%/tlara_tRNA_aln51.output
+%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb169168.1
+%%EXAMPLESDIR%%/tmp_file_for_extract_from_pdb89508.1
+%%EXAMPLESDIR%%/two_profiles.template_file
%%DATADIR%%/license.txt
%%DATADIR%%/html/t_coffee.html
%%DATADIR%%/html/t_coffee4html.cgi
- at dirrmtry %%DOCSDIR%%
+%%PORTDOCS%%@dirrmtry %%DOCSDIR%%
@dirrmtry %%EXAMPLESDIR%%
@dirrm %%DATADIR%%/html
@dirrmtry %%DATADIR%%
>Release-Note:
>Audit-Trail:
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