[med-svn] r1727 - in trunk/packages/t-coffee/trunk/debian: . patches
charles-guest at alioth.debian.org
charles-guest at alioth.debian.org
Wed Apr 9 13:24:24 UTC 2008
Author: charles-guest
Date: 2008-04-09 13:24:22 +0000 (Wed, 09 Apr 2008)
New Revision: 1727
Added:
trunk/packages/t-coffee/trunk/debian/compat
trunk/packages/t-coffee/trunk/debian/control
trunk/packages/t-coffee/trunk/debian/patches/unicode.diff
trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical
trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial
trunk/packages/t-coffee/trunk/debian/t-coffee.install
trunk/packages/t-coffee/trunk/debian/t-coffee.manpages
trunk/packages/t-coffee/trunk/debian/t_coffee.1
Removed:
trunk/packages/t-coffee/trunk/debian/compat
trunk/packages/t-coffee/trunk/debian/control
trunk/packages/t-coffee/trunk/debian/patches/manpage.patch
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/patches/dmcoffee.patch
trunk/packages/t-coffee/trunk/debian/patches/series
trunk/packages/t-coffee/trunk/debian/rules
Log:
New upstream version, switched to CDBS, updated doc-base sections, using dialign-tx instead of dialign-t for m-coffee.
Modified: trunk/packages/t-coffee/trunk/debian/README.Debian
===================================================================
--- trunk/packages/t-coffee/trunk/debian/README.Debian 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/README.Debian 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1,23 +1,21 @@
-t-coffee for Debian
+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.
+T-COFFEE comes with a special mode, M-COFFEE, that makes it possible to combine
+the output of many multiple sequence alignment packages. In its published
+version, it uses MUSCLE, PROBCONS, POA, DiAlign-T, MAFFT, Clustal W, PCMA and
+T-Coffee. A special version has been made for Debian, DM-Coffee, that uses
+only free software by replacing Clustal W by Kalign. Using the 8 Methods of
+M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite
+methods if you prefer. This version of T-COFFEE has been patched to use the
+latest program of the DiAlign family, DiAlign-TX.
-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
-and also for the proper description of the accompaning documention in the
-doc-base file. Another issue that comes to mind is the watch file that
-is no longer working for upstream's
- http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+To install all the necessary programs for running DM-COFFEE, you can run use
+the option `~Rsuggests:^package$' of the `aptitude' package manager, or the
+command `apt-get -o APT::Install-Suggests=true install'. In order to download
+clustalw for M-COFFEE, please add the non-free section in the file
+/etc/apt/sources.list (it has a man page).
-The example directory became a separate package and so are the docs. This
-was motivated by the idea to use Debian packages on compute clusters and
-hence, well, one wants them space-minimal or close to it, at least.
-
Whenever appropriate please cite this software as
3DCoffee: Combining Protein Sequences and Structures within
@@ -38,6 +36,8 @@
C. Notredame, L. Holme and D.G. Higgins, Bioinformatics, Vol 14
(5) 407-422, 1998
-Steffen
+and/or
- -- Steffen Moeller <moeller at debian.org> Mon, 24 Sep 2007 15:05:07 +0200
+ M-Coffee: combining multiple sequence alignment methods with T-Coffee.
+ Wallace IM, O'Sullivan O, Higgins DG, Notredame C. Nucleic Acids Res.
+ 2006 Mar 23;34(6):1692-9.
Modified: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/changelog 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1,11 +1,14 @@
-t-coffee (5.57-1) UNRELEASED; urgency=low
+t-coffee (5.68-1) UNRELEASED; urgency=low
[ David Paleino ]
* New upstream release
* Added myself to Uploaders
- * Minor changes to debian/rules
[ Charles Plessy ]
+ * Switched to CDBS.
+ * debian/patches:
+ - Unicode conversions.
+ - Upated the dm-coffee patch because dialign-t was renamed dialign-tx
* Changed the doc-base section according to the new policy.
-- Charles Plessy <charles-debian-nospam at plessy.org> Sat, 22 Mar 2008 11:10:30 +0900
Deleted: trunk/packages/t-coffee/trunk/debian/compat
===================================================================
--- trunk/packages/t-coffee/trunk/debian/compat 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/compat 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1 +0,0 @@
-5
Added: trunk/packages/t-coffee/trunk/debian/compat
===================================================================
--- trunk/packages/t-coffee/trunk/debian/compat (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/compat 2008-04-09 13:24:22 UTC (rev 1727)
@@ -0,0 +1 @@
+5
Deleted: trunk/packages/t-coffee/trunk/debian/control
===================================================================
--- trunk/packages/t-coffee/trunk/debian/control 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/control 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1,45 +0,0 @@
-Source: t-coffee
-Section: science
-Priority: optional
-Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
-Uploaders: Steffen Moeller <moeller at debian.org>,
- Charles Plessy <charles-debian-nospam at plessy.org>,
- David Paleino <d.paleino at gmail.com>
-Build-Depends: debhelper (>= 5), quilt
-Standards-Version: 3.7.3
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/t-coffee/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/t-coffee/trunk/
-Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-
-Package: t-coffee
-Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: clustalw, dialign-t, kalign, mafft, muscle, poa, probcons, seaview, boxshade, t-coffee-doc
-Description: Multiple Sequence Alignment
- T-Coffee is a multiple sequence alignment package. Given a set of
- sequences (Proteins or DNA), T-Coffee generates a multiple sequence
- alignment. Version 2.00 and higher can mix sequences and structures.
- .
- T-Coffee allows the combination of a collection of multiple/pairwise,
- global or local alignments into a single model. It also allows to
- estimate the level of consistency of each position within the new
- alignment with the rest of the alignments. See the pre-print for more
- information
-
-Package: t-coffee-examples
-Architecture: all
-Recommends: t-coffee
-Description: annotated examples for the use of T-Coffee
- To help increasing the proficiency in the use of T-Coffee, this
- package provides examples for input sequences and their proper
- alignment.
-
-Package: t-coffee-doc
-Architecture: all
-Section: doc
-Recommends: t-coffee
-Suggests: t-coffee-examples
-Description: PDF and HTML accompaning documents to T-Coffee
- The tool for multiple sequence alignment, T-Coffee, is explained
- both from the users' perspective and for its technical background.
Added: trunk/packages/t-coffee/trunk/debian/control
===================================================================
--- trunk/packages/t-coffee/trunk/debian/control (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/control 2008-04-09 13:24:22 UTC (rev 1727)
@@ -0,0 +1,54 @@
+Source: t-coffee
+Section: science
+Priority: optional
+Maintainer: Debian-Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Steffen Moeller <moeller at debian.org>,
+ Charles Plessy <charles-debian-nospam at plessy.org>,
+ David Paleino <d.paleino at gmail.com>
+Build-Depends: debhelper (>= 5), cdbs, quilt
+Standards-Version: 3.7.3
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/t-coffee/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/t-coffee/trunk/
+Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+
+Package: t-coffee
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: boxshade, seaview, t-coffee-doc, t-coffee-examples
+ dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw
+Description: Multiple Sequence Alignment
+ T-Coffee is a multiple sequence alignment package. Given a set of
+ sequences (Proteins or DNA), T-Coffee generates a multiple sequence
+ alignment. Version 2.00 and higher can mix sequences and structures.
+ .
+ T-Coffee allows the combination of a collection of multiple/pairwise,
+ global or local alignments into a single model. It also allows to
+ estimate the level of consistency of each position within the new
+ alignment with the rest of the alignments. See the pre-print for more
+ information
+ .
+ T-Coffee has a special called M-Coffee that makes it possible to combine the
+ output of many multiple sequence alignment packages. In its published version,
+ it uses MUSCLE, PROBCONS, POA, DiAlign-TS, MAFFT, Clustal W, PCMA and
+ T-Coffee. A special version has been made for Debian, DM-Coffee, that uses
+ only free software by replacing Clustal W by Kalign. Using the 8 Methods of
+ M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite
+ methods if you prefer.
+
+Package: t-coffee-examples
+Architecture: all
+Recommends: t-coffee
+Description: annotated examples for the use of T-Coffee
+ To help increasing the proficiency in the use of T-Coffee, this
+ package provides examples for input sequences and their proper
+ alignment.
+
+Package: t-coffee-doc
+Architecture: all
+Section: doc
+Recommends: t-coffee
+Suggests: t-coffee-examples
+Description: PDF and HTML accompaning documents to T-Coffee
+ The tool for multiple sequence alignment, T-Coffee, is explained
+ both from the users' perspective and for its technical background.
Modified: trunk/packages/t-coffee/trunk/debian/copyright
===================================================================
--- trunk/packages/t-coffee/trunk/debian/copyright 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/copyright 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1,11 +1,13 @@
-T-Coffee was downloaded from http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
-This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
-Fri, 13 May 2005 10:52:14 +0200.
+X-Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat
+X-Debianized-By: Steffen Moeller <moeller at pzr.uni-rostock.de>
+X-Debianized-Date: Fri, 13 May 2005 10:52:14 +0200
+X-Source-Downloaded-From: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html
+X-Upstream-Author: Cédric Notredame <cedric.notredame at europe.com>
Files: debian/*
Copyright: © 2005-2007 Steffen Möller <moeller at debian.org>
License: unknown
-Copyright: © 2006-2007 Charles Plessy <charles-debian-nospam at plessy.org>
+Copyright: © 2006-2008 Charles Plessy <charles-debian-nospam at plessy.org>
License: same as T-Coffee itself
Files: *
@@ -16,15 +18,15 @@
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.
-.
+ .
T-COFFEE is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
-.
- You should have received a copy of the GNU General Public License
- along with this package; if not, write to the Free Software
- Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
+ .
+ You should have received a copy of the GNU General Public License
+ along with this package; if not, write to the Free Software
+ Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA
-On Debian systems, the complete text of the GNU General
+X-Comment: On Debian systems, the complete text of the GNU General
Public License can be found in `/usr/share/common-licenses/GPL'.
Modified: trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/patches/dmcoffee.patch 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1,27 +1,38 @@
If we do not hardcode these paths, dmcoffee will not work out of the box.
-Index: T-COFFEE_distribution_Version_5.31/t_coffee_source/util_constraints_list.c
-===================================================================
---- T-COFFEE_distribution_Version_5.31.orig/t_coffee_source/util_constraints_list.c
-+++ T-COFFEE_distribution_Version_5.31/t_coffee_source/util_constraints_list.c
-@@ -1306,7 +1306,7 @@
+--- a/t_coffee_source/util_constraints_list.c
++++ b/t_coffee_source/util_constraints_list.c
+@@ -1368,13 +1368,13 @@
+ else if ( lstrstr ( method, "dialignt_pair"))
+ {
+
+- check_program_is_installed ("dialign-t", NULL, NULL, "http://dialign-t.gobics.de/", IS_FATAL);
++ check_program_is_installed ("dialign-tx", NULL, NULL, "http://dialign-tx.gobics.de/", IS_FATAL);
+
+ fp=vfopen (fname, "w");
fprintf ( fp, "EXECUTABLE %s\n",(getenv("DIALIGNT_4_TCOFFEE"))?getenv("DIALIGNT_4_TCOFFEE"):DIALIGNT_4_TCOFFEE );
fprintf ( fp, "ALN_MODE pairwise\n");
fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
-+ fprintf ( fp, "PARAM1 /usr/share/dialign-t \n", get_mcoffee_4_tcoffee());
++ fprintf ( fp, "PARAM1 /usr/share/dialign-tx \n", get_mcoffee_4_tcoffee());
fprintf ( fp, "IN_FLAG &bnsp\n");
fprintf ( fp, "OUT_FLAG &bnsp\n");
fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
-@@ -1324,7 +1324,7 @@
+@@ -1387,12 +1387,12 @@
+ else if ( lstrstr ( method, "dialignt_msa"))
+ {
+
+- check_program_is_installed ("dialign-t", NULL, NULL, "http://dialign-t.gobics.de/", IS_FATAL);
++ check_program_is_installed ("dialign-tx", NULL, NULL, "http://dialign-tx.gobics.de/", IS_FATAL);
+ fp=vfopen (fname, "w");
fprintf ( fp, "EXECUTABLE %s\n",(getenv("DIALIGNT_4_TCOFFEE"))?getenv("DIALIGNT_4_TCOFFEE"):DIALIGNT_4_TCOFFEE );
fprintf ( fp, "ALN_MODE multiple\n");
fprintf ( fp, "OUT_MODE aln\n");
- fprintf ( fp, "PARAM1 %s \n", get_mcoffee_4_tcoffee());
-+ fprintf ( fp, "PARAM1 /usr/share/dialign-t \n", get_mcoffee_4_tcoffee());
++ fprintf ( fp, "PARAM1 /usr/share/dialign-tx \n", get_mcoffee_4_tcoffee());
fprintf ( fp, "IN_FLAG &bnsp\n");
fprintf ( fp, "OUT_FLAG &bnsp\n");
fprintf ( fp, "PARAM >/dev/null&bnsp2>/dev/null\n");
-@@ -1346,7 +1346,7 @@
+@@ -1414,7 +1414,7 @@
fprintf ( fp, "PARAM1 -toupper \n");
fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n");
fprintf ( fp, "OUT_FLAG -clustal&bnsp\n");
@@ -30,7 +41,7 @@
fprintf ( fp, "SEQ_TYPE S\n");
vfclose (fp);
-@@ -1364,7 +1364,7 @@
+@@ -1432,7 +1432,7 @@
fprintf ( fp, "PARAM1 -toupper \n");
fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n");
fprintf ( fp, "OUT_FLAG -clustal&bnsp\n");
Deleted: trunk/packages/t-coffee/trunk/debian/patches/manpage.patch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/manpage.patch 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/patches/manpage.patch 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1,235 +0,0 @@
-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).
Modified: trunk/packages/t-coffee/trunk/debian/patches/series
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/series 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/patches/series 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1,3 +1,3 @@
dmcoffee.patch
-manpage.patch
Makefiles.patch
+unicode.diff
Added: trunk/packages/t-coffee/trunk/debian/patches/unicode.diff
===================================================================
--- trunk/packages/t-coffee/trunk/debian/patches/unicode.diff (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/patches/unicode.diff 2008-04-09 13:24:22 UTC (rev 1727)
@@ -0,0 +1,93 @@
+--- a/doc/t_coffee_technical.txt
++++ b/doc/t_coffee_technical.txt
+@@ -4,7 +4,7 @@
+ Centre National De LA Recherche scientifique (France)
+
+ CeNTRO De REGULACIO GENOMICA (SPAIN)
+-Cédric Notredame
++Cédric Notredame
+
+ www.tcoffee.org
+
+@@ -32,7 +32,7 @@
+
+ APDB and iRMSD
+
+- ( Cédric Notredame and Centre National de la Recherche Scientifique, France
++ ( Cédric Notredame and Centre National de la Recherche Scientifique, France
+ License and Terms of Use 5
+ T-Coffee is distributed under the Gnu Public License 5
+ T-Coffee code can be re-used freely 5
+@@ -302,7 +302,7 @@
+ T-coffee is developed, maintained, monitored, used and debugged by a
+ dedicated team that include:
+
+- Cédric Notredame
++ Cédric Notredame
+
+ Fabrice Armougom
+
+@@ -1315,7 +1315,7 @@
+ Forces t_coffee to identify the sequences type (PROTEIN, DNA).
+
+ -type [cw]
+- Usage: -type=DNA ¦ PROTEIN¦ DNA_PROTEIN
++ Usage: -type=DNA Å PROTEINÅ DNA_PROTEIN
+ Default: -type=<automatically set>
+
+ This flag sets the type of the sequences. If omitted, the type is
+--- a/doc/t_coffee_tutorial.txt
++++ b/doc/t_coffee_tutorial.txt
+@@ -2,7 +2,7 @@
+ T-coffee Tutorial
+
+ Centre National De LA Recherche scientifique
+-Cédric Notredame
++Cédric Notredame
+
+ www.tcoffee.org
+
+@@ -26,7 +26,7 @@
+
+ APDB and iRMSD
+
+- ( Cédric Notredame and Centre National de la Recherche Scientifique, France
++ ( Cédric Notredame and Centre National de la Recherche Scientifique, France
+ Before You Start. 5
+ Foreword 5
+ Pre-Requisite 5
+@@ -1693,11 +1693,11 @@
+ each of these applications with T-Coffee.
+
+ | |Muscle |Mafft |
+-|Expresso |sproteases_small.expresso|1.33 Å |
+-|T-Coffee |sproteases_small.tc_aln |1.35 Å |
+-|ClustalW |sproteases_small.cw_aln |1.52 Å |
+-|Mafft |sproteases_small.mafft |1.36 Å |
+-|Muscle |sproteases_small.muscle |1.34 Å |
++|Expresso |sproteases_small.expresso|1.33 Ã… |
++|T-Coffee |sproteases_small.tc_aln |1.35 Ã… |
++|ClustalW |sproteases_small.cw_aln |1.52 Ã… |
++|Mafft |sproteases_small.mafft |1.36 Ã… |
++|Muscle |sproteases_small.muscle |1.34 Ã… |
+
+
+ As expected, Expresso delivers the best alignment from a structural
+@@ -2112,7 +2112,7 @@
+ This special method (em, external method) uses the following syntax:
+
+
+- em@<method>@<aln_mode:pairwise¦s_pairwise|multiple>
++ em@<method>@<aln_mode:pairwiseÅ s_pairwise|multiple>
+
+
+ 2 Customizing an external method (with parameters) for T-Coffee
+@@ -3307,7 +3307,7 @@
+ T-coffee is developed, maintained, monitored, used and debugged by a
+ dedicated team that include:
+
+- Cédric Notredame
++ Cédric Notredame
+
+ Fabrice Armougom
+
Modified: trunk/packages/t-coffee/trunk/debian/rules
===================================================================
--- trunk/packages/t-coffee/trunk/debian/rules 2008-04-09 10:09:22 UTC (rev 1726)
+++ trunk/packages/t-coffee/trunk/debian/rules 2008-04-09 13:24:22 UTC (rev 1727)
@@ -1,84 +1,15 @@
#!/usr/bin/make -f
-# -*- makefile -*-
-# Sample debian/rules that uses debhelper.
-# This file was originally written by Joey Hess and Craig Small.
-# As a special exception, when this file is copied by dh-make into a
-# dh-make output file, you may use that output file without restriction.
-# This special exception was added by Craig Small in version 0.37 of dh-make.
-# Uncomment this to turn on verbose mode.
-#export DH_VERBOSE=1
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk
-include /usr/share/quilt/quilt.make
+# DEB_SRCDIR = t_coffee_source
+# Is messing with /usr/share/cdbs/1/rules/patchsys-quilt.mk
-CFLAGS = -Wall -g
+DEB_MAKE_BUILD_TARGET = -C t_coffee_source -i USER_BIN=../bin/ all
+DEB_MAKE_CLEAN_TARGET = -C t_coffee_source clean
-ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
- CFLAGS += -O0
-else
- CFLAGS += -O2
-endif
-
-build: build-stamp
-build-stamp: patch
- dh_testdir
- $(MAKE) -C t_coffee_source -i CC=gcc CFLAGS="$(CFLAGS)" USER_BIN=../bin/ all
- touch $@
-
-clean: unpatch
- dh_testdir
- dh_testroot
- rm -f build-stamp configure-stamp
- # circumventing a hen-and-egg problem
- # the fix to clean the source even if not necessary is only applied after the clean
- [ -r t_coffee_source/util_dp_drivers.o ] && $(MAKE) -C t_coffee_source clean || echo No need to clean the source
- dh_clean bin/t_coffee `find example/ -size 0` doc/t_coffee.pdf
-
-install: install-arch install-indep
-
-install-arch: build
- dh_testdir
- dh_testroot
- dh_clean -k
- dh_installdirs
- dh_install
- # Add here commands to install the package into debian/t-coffee.
- d=$(CURDIR)/debian/t-coffee/usr/bin/ ; \
- [ -d $$d ] || mkdir -p $$d ; \
- cp bin/t_coffee $$d
-
-install-indep:
-
-binary-indep: build install-indep
- dh_testdir
- dh_testroot
- dh_installchangelogs -pt-coffee-examples -pt-coffee-doc
- dh_installdocs -pt-coffee-examples -pt-coffee-doc
+clean::
+ dh_clean bin/t_coffee $(shell find example/ -size 0)
chmod 644 example/*
- dh_installexamples -pt-coffee-examples example/*
- dh_link -pt-coffee-examples -pt-coffee-doc
- dh_compress -pt-coffee-examples -pt-coffee-doc
- dh_fixperms -pt-coffee-examples -pt-coffee-doc
- dh_installdeb -pt-coffee-examples -pt-coffee-doc
- dh_gencontrol -pt-coffee-examples -pt-coffee-doc
- dh_md5sums -pt-coffee-examples -pt-coffee-doc
- dh_builddeb -pt-coffee-examples -pt-coffee-doc
-
-binary-arch: build install-arch
- dh_testdir
- dh_testroot
- dh_installchangelogs
- dh_installdocs
- dh_installman -pt-coffee t_coffee.1
- dh_link
- dh_strip
- dh_compress
- dh_fixperms -pt-coffee
- dh_installdeb -pt-coffee
- dh_shlibdeps -pt-coffee
- dh_gencontrol -pt-coffee
- dh_md5sums -pt-coffee
- dh_builddeb -pt-coffee
-
-binary: binary-indep binary-arch
-.PHONY: build clean binary-indep binary-arch binary install
Copied: trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical (from rev 1337, trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base)
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.technical 2008-04-09 13:24:22 UTC (rev 1727)
@@ -0,0 +1,12 @@
+Document: t-coffee
+Title: Debian t-coffee Manual
+Author: Cédric Notredame
+Abstract: A description of T-Coffee, the program
+ for multiple sequence alignment, and sequence
+ formats. The documentation entails both a technical
+ description and a tutorial for a novice's first
+ steps.
+Section: Applications/Science/Biology
+
+Format: text
+Files: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.txt.gz /usr/share/doc/t-coffee-doc/t_coffee_technical.txt.gz
Copied: trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial (from rev 1337, trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base)
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee-doc.doc-base.tutorial 2008-04-09 13:24:22 UTC (rev 1727)
@@ -0,0 +1,12 @@
+Document: t-coffee
+Title: Debian t-coffee Manual
+Author: Cédric Notredame
+Abstract: A description of T-Coffee, the program
+ for multiple sequence alignment, and sequence
+ formats. The documentation entails both a technical
+ description and a tutorial for a novice's first
+ steps.
+Section: Applications/Science/Biology
+
+Format: text
+Files: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.txt.gz /usr/share/doc/t-coffee-doc/t_coffee_technical.txt.gz
Added: trunk/packages/t-coffee/trunk/debian/t-coffee.install
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee.install (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee.install 2008-04-09 13:24:22 UTC (rev 1727)
@@ -0,0 +1 @@
+bin/t_coffee /usr/bin
Added: trunk/packages/t-coffee/trunk/debian/t-coffee.manpages
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee.manpages (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee.manpages 2008-04-09 13:24:22 UTC (rev 1727)
@@ -0,0 +1 @@
+debian/t_coffee.1
Added: trunk/packages/t-coffee/trunk/debian/t_coffee.1
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t_coffee.1 (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t_coffee.1 2008-04-09 13:24:22 UTC (rev 1727)
@@ -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).
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