[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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