[med-svn] r452 - in trunk/packages/t-coffee/trunk: . debian debian/patches

smoe-guest at alioth.debian.org smoe-guest at alioth.debian.org
Mon Sep 24 14:22:50 UTC 2007


Author: smoe-guest
Date: 2007-09-24 14:22:50 +0000 (Mon, 24 Sep 2007)
New Revision: 452

Added:
   trunk/packages/t-coffee/trunk/debian/patches/
   trunk/packages/t-coffee/trunk/debian/patches/Makefiles.patch
   trunk/packages/t-coffee/trunk/debian/patches/manpage.patch
   trunk/packages/t-coffee/trunk/debian/patches/series
Removed:
   trunk/packages/t-coffee/trunk/t_coffee.1
   trunk/packages/t-coffee/trunk/t_coffee_source/
Modified:
   trunk/packages/t-coffee/trunk/debian/README.Debian
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/copyright
   trunk/packages/t-coffee/trunk/debian/docs
   trunk/packages/t-coffee/trunk/debian/rules
Log:
Some cleanups to adapt T-Coffee for the latest version.



Modified: trunk/packages/t-coffee/trunk/debian/README.Debian
===================================================================
--- trunk/packages/t-coffee/trunk/debian/README.Debian	2007-09-24 13:00:29 UTC (rev 451)
+++ trunk/packages/t-coffee/trunk/debian/README.Debian	2007-09-24 14:22:50 UTC (rev 452)
@@ -1,26 +1,37 @@
 t-coffee for Debian
 -------------------
 
+The previous version in the archive has several problems, hence this
+long overdue update. Nobody has pointed me to the new upstream version,
+it was only me in routine preparation for some bug reports that I had checked
+for an update. Well, time is floating.
+
+The web interface in the folder html I decided to leave as it is and move
+aside the regular documentation. I have not updated the man page from the
+previous version yet. Some helping hands would be welcome in this matter.
+
+The example directory was omitted. Should this become a separate package?
+
 Whenever appropriate please cite this software as
 
 	3DCoffee: Combining Protein Sequences and Structures within
 	Multiple Sequence Alignments.
 	 O. O'Sullivan, K Suhre, C. Abergel, D.G. Higgins,
-	 C. Notredame. Journal of Molecular Biology,Vol 340,
-	 pp385-395,2004[pdf]
+	 C. Notredame. Journal of Molecular Biology, Vol 340,
+	 pp385-395, 2004
 
 or
 
 	T-Coffee: A novel method for multiple sequence alignments.
-	C.Notredame, D. Higgins, J. Heringa,Journal of Molecular
-	Biology,Vol 302, pp205-217,2000[pdf]
+	C.Notredame, D. Higgins, J. Heringa, Journal of Molecular
+	Biology,Vol 302, pp205-217, 2000
 
 or
 
 	COFFEE: A New Objective Function For Multiple Sequence Alignmnent.
-	C. Notredame, L. Holme and D.G. Higgins,Bioinformatics,Vol 14
-	(5) 407-422,1998[pdf]
+	C. Notredame, L. Holme and D.G. Higgins, Bioinformatics, Vol 14
+	(5) 407-422, 1998
 
 Steffen
 
- -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Fri, 13 May 2005 10:52:14 +0200
+ -- Steffen Moeller <moeller at debian.org>  Mon, 24 Sep 2007 15:05:07 +0200

Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog	2007-09-24 13:00:29 UTC (rev 451)
+++ trunk/packages/t-coffee/trunk/debian/changelog	2007-09-24 14:22:50 UTC (rev 452)
@@ -1,3 +1,10 @@
+t-coffee (5.05) unstable; urgency=low
+
+  * New upstream version.
+  * Added use of quilt.
+
+ -- Steffen Moeller <moeller at debian.org>  Mon, 24 Sep 2007 15:05:07 +0200
+
 t-coffee (2.50-1) unstable; urgency=low
 
   * Initial Release (Closes: Bug#205370).

Modified: trunk/packages/t-coffee/trunk/debian/copyright
===================================================================
--- trunk/packages/t-coffee/trunk/debian/copyright	2007-09-24 13:00:29 UTC (rev 451)
+++ trunk/packages/t-coffee/trunk/debian/copyright	2007-09-24 14:22:50 UTC (rev 452)
@@ -3,14 +3,14 @@
 
 It was downloaded from http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html
 
-Copyright Holder: Cedric Notredame <cedric.notredame at europe.com>
+Copyright Holder: Centre National de la Recherche Scientifique (CNRS) 
+                  and Cedric Notredame <cedric.notredame at europe.com>
 
 License:
 
    This package is free software; you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
-   the Free Software Foundation; either version 2 of the License, or
-   (at your option) any later version.
+   the Free Software Foundation; either version 2 of the License.
 
    This package is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of

Modified: trunk/packages/t-coffee/trunk/debian/docs
===================================================================
--- trunk/packages/t-coffee/trunk/debian/docs	2007-09-24 13:00:29 UTC (rev 451)
+++ trunk/packages/t-coffee/trunk/debian/docs	2007-09-24 14:22:50 UTC (rev 452)
@@ -1,6 +1,3 @@
 doc/README4T-COFFEE
-doc/aln_compare.doc.txt
-doc/seq_reformat.doc.txt
-doc/t_coffee.pdf
-doc/t_coffee_doc.pdf
-doc/t_coffee_doc.txt
+doc/*.htm
+html

Added: trunk/packages/t-coffee/trunk/debian/patches/Makefiles.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/Makefiles.patch	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/patches/Makefiles.patch	2007-09-24 14:22:50 UTC (rev 452)
@@ -0,0 +1,10 @@
+Index: t-coffee-5.05/t_coffee_source/makefile
+===================================================================
+--- t-coffee-5.05.orig/t_coffee_source/makefile	2007-09-24 15:26:47.028236512 +0200
++++ t-coffee-5.05/t_coffee_source/makefile	2007-09-24 15:27:26.136696266 +0200
+@@ -6,4 +6,4 @@
+ all:  t_coffee
+ 
+ clean:
+-	rm *.o
++	rm -f *.o t_coffee

Added: trunk/packages/t-coffee/trunk/debian/patches/manpage.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/manpage.patch	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/patches/manpage.patch	2007-09-24 14:22:50 UTC (rev 452)
@@ -0,0 +1,235 @@
+Index: t-coffee-5.05/t_coffee.1
+===================================================================
+--- /dev/null	1970-01-01 00:00:00.000000000 +0000
++++ t-coffee-5.05/t_coffee.1	2007-09-24 15:18:51.578647190 +0200
+@@ -0,0 +1,230 @@
++.\"                                      Hey, EMACS: -*- nroff -*-
++.TH T-COFFEE 1 "May 13, 2005"
++.SH NAME
++t-coffee \- multiple sequence alignment
++.SH SYNOPSIS
++.B t_coffee
++.RI [ options ] file
++.br
++.PP
++\fBt-coffee\fP aligns multiple DNA or protein sequences.
++.SH OPTIONS
++A summary of options is included below.
++For a complete description, see the documentation.
++.TP
++.B -full_log       S       [0]
++.TP
++.B -run_name       S       [0]
++.TP
++.B -mem_mode       S       [0]     mem
++.TP
++.B -extend         D       [1]     1
++.TP
++.B -extend_mode    S       [0]     very_fast_triplet
++.TP
++.B -max_n_pair     D       [0]     10
++.TP
++.B -seq_name_for_quadruplet        S       [0]     all
++.TP
++.B -compact        S       [0]     default
++.TP
++.B -clean          S       [0]     no
++.TP
++.B -do_self        FL      [0]     0
++.TP
++.B -do_normalise   D       [0]     1000
++.TP
++.B -template_file  S       [0]
++.TP
++.B -seq            S       [0]
++.TP
++.B -in             S       [0]     Mlalign_id_pair Mslow_pair
++.TP
++.B -pdb            S       [0]
++.TP
++.B -out_lib        W_F     [0]     no
++.TP
++.B -lib_only       D       [0]     0
++.TP
++.B -outseqweight   W_F     [0]     no
++.TP
++.B -seq_source     S       [0]     ANY
++.TP
++.B -cosmetic_penalty       D       [0]     -50
++.TP
++.B -gapopen        D       [0]     0
++.TP
++.B -gapext         D       [0]     0
++.TP
++.B -fgapopen       D       [0]     0
++.TP
++.B -fgapext        D       [0]     0
++.TP
++.B -nomatch        D       [0]     0
++.TP
++.B -newtree        W_F     [0]     default
++.TP
++.B -usetree        R_F     [0]
++.TP
++.B -tree_mode      S       [0]     slow
++.TP
++.B -quicktree      FL      [0]     0
++.TP
++.B -outfile        W_F     [0]     default
++.TP
++.B -maximise       FL      [1]     1
++.TP
++.B -output         S       [0]     clustalw
++.TP
++.B -infile         R_F     [0]
++.TP
++.B -matrix         S       [0]     blosum62mt
++.TP
++.B -tg_mode        D       [0]     1
++.TP
++.B -profile_mode   S       [0]     cw_profile_profile
++.TP
++.B -profile_comparison     S       [0]     full50
++.TP
++.B -dp_mode        S       [0]     cfasta_pair_wise
++.TP
++.B -ktuple         D       [0]     1
++.TP
++.B -ndiag          D       [0]     0
++.TP
++.B -diag_threshold D       [0]     0
++.TP
++.B -diag_mode      D       [0]     0
++.TP
++.B -sim_matrix     S       [0]     vasiliky
++.TP
++.B -type           S       [0]
++.TP
++.B -outorder       S       [0]     aligned
++.TP
++.B -seqnos         S       [0]     off
++.TP
++.B -case           S       [0]     keep
++.TP
++.B -cpu            D       [0]     0
++.TP
++.B -maxnseq        D       [0]     60
++.TP
++.B -maxlen         D       [0]     -1
++.TP
++.B -weight         S       [0]     default
++.TP
++.B -seq_weight     S       [0]     t_coffee
++.TP
++.B -align          FL      [1]     1
++.TP
++.B -mocca          FL      [0]     0
++.TP
++.B -domain         FL      [0]     0
++.TP
++.B -start          D       [0]     0
++.TP
++.B -len            D       [0]     0
++.TP
++.B -scale          D       [0]     0
++.TP
++.B -mocca_interactive      FL      [0]     0
++.TP
++.B -evaluate_mode  S       [0]     t_coffee_fast
++.TP
++.B -get_type       FL      [0]     0
++.TP
++.B -clean_aln      D       [0]     0
++.TP
++.B -clean_threshold        D       [1]     1
++.TP
++.B -clean_iteration        D       [1]     1
++.TP
++.B -clean_evaluate_mode    S       [0]     t_coffee_fast
++.TP
++.B -profile        S       [0]
++.TP
++.B -profile1       S       [0]
++.TP
++.B -profile2       S       [0]
++.TP
++.B -extend_matrix  FL      [0]     0
++.TP
++.B -prot_min_sim   D       [40]    40
++.TP
++.B -prot_max_sim   D       [60]    60
++.TP
++.B -prot_min_cov   D       [0]     0
++.TP
++.B -pdb_min_sim    D       [30]    30
++.TP
++.B -pdb_max_sim    D       [100]   100
++.TP
++.B -pdb_min_cov    D       [50]    50
++.TP
++.B -pdb_blast_server       W_F     [0]     SIB
++.TP
++.B -prot_blast_server      W_F     [0]     SIB
++.TP
++.B -pdb_db         W_F     [0]     nrl3d
++.TP
++.B -protein_db     W_F     [0]     nr
++.TP
++.B -method_log     W_F     [0]     no
++.TP
++.B -struc_to_use   S       [0]
++.TP
++.B -cache          W_F     [0]     use
++.TP
++.B -align_pdb_param_file   W_F     [0]     no
++.TP
++.B -align_pdb_hasch_mode   W_F     [0]     hasch_ca_trace_bubble
++.TP
++.B -msa_mode       S       [0]     tree
++.TP
++.B -lalign_n_top   D       [0]     10
++.TP
++.B -iterate        D       [0]     0
++.TP
++.B -trim           D       [0]     0
++.TP
++.B -split          D       [0]     0
++.TP
++.B -trimfile       S       [0]     default
++.TP
++.B -split          D       [0]     0
++.TP
++.B -split_nseq_thres       D       [0]     0
++.TP
++.B -split_score_thres      D       [0]     0
++.TP
++.B -check_pdb_status       D       [0]     0
++.TP
++.B -seq_to_keep    S       [0]
++.TP
++.B -dpa_master_aln S       [0]
++.TP
++.B -dpa_maxnseq    D       [0]     10
++.TP
++.B -dpa_min_score1 D       [0]
++.TP
++.B -dpa_min_score2 D       [0]
++.TP
++.B -dpa_keep_tmpfile       FL      [0]     0
++.TP
++.B -dpa_debug      D       [0]     0
++.TP
++.B -multi_thread   S       [0]
++.TP
++.B -lib_list       S       [0]
++
++.SH SEE ALSO
++.BR clustalw (1),
++.BR /usr/share/doc/t-coffee/,
++.br
++.BR http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home
++.SH AUTHOR
++t-coffee was written by Cedric Notredame <cedric.notredame at europe.com>
++.PP
++This manual page was written by Steffen Moeller <moeller at pzr.uni-rostock.de>,
++for the Debian project (but may be used by others).

Added: trunk/packages/t-coffee/trunk/debian/patches/series
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/series	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/patches/series	2007-09-24 14:22:50 UTC (rev 452)
@@ -0,0 +1,2 @@
+manpage.patch
+Makefiles.patch

Modified: trunk/packages/t-coffee/trunk/debian/rules
===================================================================
--- trunk/packages/t-coffee/trunk/debian/rules	2007-09-24 13:00:29 UTC (rev 451)
+++ trunk/packages/t-coffee/trunk/debian/rules	2007-09-24 14:22:50 UTC (rev 452)
@@ -10,8 +10,8 @@
 #export DH_VERBOSE=1
 
 
+include /usr/share/quilt/quilt.make
 
-
 CFLAGS = -Wall -g
 
 ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
@@ -23,7 +23,7 @@
 configure: 
 	# Nothing to configure
 	
-build: build-stamp
+build: patch build-stamp
 
 build-stamp: 
 	dh_testdir
@@ -34,7 +34,7 @@
 
 	touch build-stamp
 
-clean:
+clean:  unpatch
 	dh_testdir
 	dh_testroot
 	rm -f build-stamp configure-stamp

Deleted: trunk/packages/t-coffee/trunk/t_coffee.1
===================================================================
--- trunk/packages/t-coffee/trunk/t_coffee.1	2007-09-24 13:00:29 UTC (rev 451)
+++ trunk/packages/t-coffee/trunk/t_coffee.1	2007-09-24 14:22:50 UTC (rev 452)
@@ -1,230 +0,0 @@
-.\"                                      Hey, EMACS: -*- nroff -*-
-.TH T-COFFEE 1 "May 13, 2005"
-.SH NAME
-t-coffee \- multiple sequence alignment
-.SH SYNOPSIS
-.B t_coffee
-.RI [ options ] file
-.br
-.PP
-\fBt-coffee\fP aligns multiple DNA or protein sequences.
-.SH OPTIONS
-A summary of options is included below.
-For a complete description, see the documentation.
-.TP
-.B -full_log       S       [0]
-.TP
-.B -run_name       S       [0]
-.TP
-.B -mem_mode       S       [0]     mem
-.TP
-.B -extend         D       [1]     1
-.TP
-.B -extend_mode    S       [0]     very_fast_triplet
-.TP
-.B -max_n_pair     D       [0]     10
-.TP
-.B -seq_name_for_quadruplet        S       [0]     all
-.TP
-.B -compact        S       [0]     default
-.TP
-.B -clean          S       [0]     no
-.TP
-.B -do_self        FL      [0]     0
-.TP
-.B -do_normalise   D       [0]     1000
-.TP
-.B -template_file  S       [0]
-.TP
-.B -seq            S       [0]
-.TP
-.B -in             S       [0]     Mlalign_id_pair Mslow_pair
-.TP
-.B -pdb            S       [0]
-.TP
-.B -out_lib        W_F     [0]     no
-.TP
-.B -lib_only       D       [0]     0
-.TP
-.B -outseqweight   W_F     [0]     no
-.TP
-.B -seq_source     S       [0]     ANY
-.TP
-.B -cosmetic_penalty       D       [0]     -50
-.TP
-.B -gapopen        D       [0]     0
-.TP
-.B -gapext         D       [0]     0
-.TP
-.B -fgapopen       D       [0]     0
-.TP
-.B -fgapext        D       [0]     0
-.TP
-.B -nomatch        D       [0]     0
-.TP
-.B -newtree        W_F     [0]     default
-.TP
-.B -usetree        R_F     [0]
-.TP
-.B -tree_mode      S       [0]     slow
-.TP
-.B -quicktree      FL      [0]     0
-.TP
-.B -outfile        W_F     [0]     default
-.TP
-.B -maximise       FL      [1]     1
-.TP
-.B -output         S       [0]     clustalw
-.TP
-.B -infile         R_F     [0]
-.TP
-.B -matrix         S       [0]     blosum62mt
-.TP
-.B -tg_mode        D       [0]     1
-.TP
-.B -profile_mode   S       [0]     cw_profile_profile
-.TP
-.B -profile_comparison     S       [0]     full50
-.TP
-.B -dp_mode        S       [0]     cfasta_pair_wise
-.TP
-.B -ktuple         D       [0]     1
-.TP
-.B -ndiag          D       [0]     0
-.TP
-.B -diag_threshold D       [0]     0
-.TP
-.B -diag_mode      D       [0]     0
-.TP
-.B -sim_matrix     S       [0]     vasiliky
-.TP
-.B -type           S       [0]
-.TP
-.B -outorder       S       [0]     aligned
-.TP
-.B -seqnos         S       [0]     off
-.TP
-.B -case           S       [0]     keep
-.TP
-.B -cpu            D       [0]     0
-.TP
-.B -maxnseq        D       [0]     60
-.TP
-.B -maxlen         D       [0]     -1
-.TP
-.B -weight         S       [0]     default
-.TP
-.B -seq_weight     S       [0]     t_coffee
-.TP
-.B -align          FL      [1]     1
-.TP
-.B -mocca          FL      [0]     0
-.TP
-.B -domain         FL      [0]     0
-.TP
-.B -start          D       [0]     0
-.TP
-.B -len            D       [0]     0
-.TP
-.B -scale          D       [0]     0
-.TP
-.B -mocca_interactive      FL      [0]     0
-.TP
-.B -evaluate_mode  S       [0]     t_coffee_fast
-.TP
-.B -get_type       FL      [0]     0
-.TP
-.B -clean_aln      D       [0]     0
-.TP
-.B -clean_threshold        D       [1]     1
-.TP
-.B -clean_iteration        D       [1]     1
-.TP
-.B -clean_evaluate_mode    S       [0]     t_coffee_fast
-.TP
-.B -profile        S       [0]
-.TP
-.B -profile1       S       [0]
-.TP
-.B -profile2       S       [0]
-.TP
-.B -extend_matrix  FL      [0]     0
-.TP
-.B -prot_min_sim   D       [40]    40
-.TP
-.B -prot_max_sim   D       [60]    60
-.TP
-.B -prot_min_cov   D       [0]     0
-.TP
-.B -pdb_min_sim    D       [30]    30
-.TP
-.B -pdb_max_sim    D       [100]   100
-.TP
-.B -pdb_min_cov    D       [50]    50
-.TP
-.B -pdb_blast_server       W_F     [0]     SIB
-.TP
-.B -prot_blast_server      W_F     [0]     SIB
-.TP
-.B -pdb_db         W_F     [0]     nrl3d
-.TP
-.B -protein_db     W_F     [0]     nr
-.TP
-.B -method_log     W_F     [0]     no
-.TP
-.B -struc_to_use   S       [0]
-.TP
-.B -cache          W_F     [0]     use
-.TP
-.B -align_pdb_param_file   W_F     [0]     no
-.TP
-.B -align_pdb_hasch_mode   W_F     [0]     hasch_ca_trace_bubble
-.TP
-.B -msa_mode       S       [0]     tree
-.TP
-.B -lalign_n_top   D       [0]     10
-.TP
-.B -iterate        D       [0]     0
-.TP
-.B -trim           D       [0]     0
-.TP
-.B -split          D       [0]     0
-.TP
-.B -trimfile       S       [0]     default
-.TP
-.B -split          D       [0]     0
-.TP
-.B -split_nseq_thres       D       [0]     0
-.TP
-.B -split_score_thres      D       [0]     0
-.TP
-.B -check_pdb_status       D       [0]     0
-.TP
-.B -seq_to_keep    S       [0]
-.TP
-.B -dpa_master_aln S       [0]
-.TP
-.B -dpa_maxnseq    D       [0]     10
-.TP
-.B -dpa_min_score1 D       [0]
-.TP
-.B -dpa_min_score2 D       [0]
-.TP
-.B -dpa_keep_tmpfile       FL      [0]     0
-.TP
-.B -dpa_debug      D       [0]     0
-.TP
-.B -multi_thread   S       [0]
-.TP
-.B -lib_list       S       [0]
-
-.SH SEE ALSO
-.BR clustalw (1),
-.BR /usr/share/doc/t-coffee/,
-.br
-.BR http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home
-.SH AUTHOR
-t-coffee was written by Cedric Notredame <cedric.notredame at europe.com>
-.PP
-This manual page was written by Steffen Moeller <moeller at pzr.uni-rostock.de>,
-for the Debian project (but may be used by others).




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