[med-svn] r451 - in trunk/packages/t-coffee/trunk: . debian t_coffee_source

smoe-guest at alioth.debian.org smoe-guest at alioth.debian.org
Mon Sep 24 13:00:29 UTC 2007


Author: smoe-guest
Date: 2007-09-24 13:00:29 +0000 (Mon, 24 Sep 2007)
New Revision: 451

Added:
   trunk/packages/t-coffee/trunk/debian/
   trunk/packages/t-coffee/trunk/debian/README.Debian
   trunk/packages/t-coffee/trunk/debian/changelog
   trunk/packages/t-coffee/trunk/debian/compat
   trunk/packages/t-coffee/trunk/debian/control
   trunk/packages/t-coffee/trunk/debian/copyright
   trunk/packages/t-coffee/trunk/debian/dirs
   trunk/packages/t-coffee/trunk/debian/docs
   trunk/packages/t-coffee/trunk/debian/install
   trunk/packages/t-coffee/trunk/debian/rules
   trunk/packages/t-coffee/trunk/debian/t-coffee.doc-base
   trunk/packages/t-coffee/trunk/debian/watch
   trunk/packages/t-coffee/trunk/t_coffee.1
Modified:
   trunk/packages/t-coffee/trunk/t_coffee_source/makefile
Log:
[svn-inject] Applying Debian modifications to trunk


Property changes on: trunk/packages/t-coffee/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
   + 1

Added: trunk/packages/t-coffee/trunk/debian/README.Debian
===================================================================
--- trunk/packages/t-coffee/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/README.Debian	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1,26 @@
+t-coffee for Debian
+-------------------
+
+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]
+
+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]
+
+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]
+
+Steffen
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>, Fri, 13 May 2005 10:52:14 +0200

Added: trunk/packages/t-coffee/trunk/debian/changelog
===================================================================
--- trunk/packages/t-coffee/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/changelog	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1,6 @@
+t-coffee (2.50-1) unstable; urgency=low
+
+  * Initial Release (Closes: Bug#205370).
+
+ -- Steffen Moeller <moeller at pzr.uni-rostock.de>  Fri, 13 May 2005 10:52:14 +0200
+

Added: trunk/packages/t-coffee/trunk/debian/compat
===================================================================
--- trunk/packages/t-coffee/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/compat	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1 @@
+4

Added: trunk/packages/t-coffee/trunk/debian/control
===================================================================
--- trunk/packages/t-coffee/trunk/debian/control	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/control	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1,24 @@
+Source: t-coffee
+Section: science
+Priority: optional
+Maintainer: Steffen Moeller <moeller at pzr.uni-rostock.de>
+Build-Depends: debhelper (>= 4.0.0)
+Standards-Version: 3.6.1
+
+Package: t-coffee
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: clustalw, muscle, seaview
+Recommends: boxshade|texshade
+Description: [Biology] 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
+ .
+  Homepage: http://igs-server.cnrs-mrs.fr/~cnotred/Projects_home_page/t_coffee_home_page.html

Added: trunk/packages/t-coffee/trunk/debian/copyright
===================================================================
--- trunk/packages/t-coffee/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/copyright	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1,27 @@
+This package was debianized by Steffen Moeller <moeller at pzr.uni-rostock.de> on
+Fri, 13 May 2005 10:52:14 +0200.
+
+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>
+
+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.
+
+   This package 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., 59 Temple Place - Suite 330, Boston, MA
+   02111-1307, USA.
+
+On Debian systems, the complete text of the GNU General
+Public License can be found in `/usr/share/common-licenses/GPL'.
+

Added: trunk/packages/t-coffee/trunk/debian/dirs
===================================================================
--- trunk/packages/t-coffee/trunk/debian/dirs	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/dirs	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1 @@
+usr/bin

Added: trunk/packages/t-coffee/trunk/debian/docs
===================================================================
--- trunk/packages/t-coffee/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/docs	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1,6 @@
+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

Added: trunk/packages/t-coffee/trunk/debian/install
===================================================================
--- trunk/packages/t-coffee/trunk/debian/install	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/install	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1 @@
+html/*.html   usr/share/doc/t-coffee/html

Added: trunk/packages/t-coffee/trunk/debian/rules
===================================================================
--- trunk/packages/t-coffee/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/rules	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1,82 @@
+#!/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
+
+
+
+
+CFLAGS = -Wall -g
+
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+	CFLAGS += -O0
+else
+	CFLAGS += -O2
+endif
+
+configure: 
+	# Nothing to configure
+	
+build: build-stamp
+
+build-stamp: 
+	dh_testdir
+
+	# Add here commands to compile the package.
+	$(MAKE) -C t_coffee_source -i CC=gcc CFLAGS="$(CFLAGS)" USER_BIN=../bin/ all
+	#docbook-to-man debian/t-coffee.sgml > t-coffee.1
+
+	touch build-stamp
+
+clean:
+	dh_testdir
+	dh_testroot
+	rm -f build-stamp configure-stamp
+
+	# Add here commands to clean up after the build process.
+	$(MAKE) -C t_coffee_source clean
+
+	dh_clean  bin/t_coffee
+
+install: build
+	dh_testdir
+	dh_testroot
+	dh_clean -k 
+	dh_installdirs
+
+	dh_install
+	# Add here commands to install the package into debian/t-coffee.
+	cp bin/t_coffee $(CURDIR)/debian/t-coffee/usr/bin/
+
+
+# Build architecture-independent files here.
+binary-indep: build install
+# We have nothing to do by default.
+
+# Build architecture-dependent files here.
+binary-arch: build install
+	dh_testdir
+	dh_testroot
+	dh_installchangelogs 
+	dh_installdocs
+	chmod 644 example/*
+	dh_installexamples example
+	dh_installman t_coffee.1
+	dh_link
+	dh_strip
+	dh_compress
+	dh_fixperms
+	dh_installdeb
+	dh_shlibdeps
+	dh_gencontrol
+	dh_md5sums
+	dh_builddeb
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install configure


Property changes on: trunk/packages/t-coffee/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
   + *

Added: trunk/packages/t-coffee/trunk/debian/t-coffee.doc-base
===================================================================
--- trunk/packages/t-coffee/trunk/debian/t-coffee.doc-base	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/t-coffee.doc-base	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1,22 @@
+Document: t-coffee
+Title: Debian t-coffee Manual
+Author: Cedric Notredame
+Abstract: A description of T-Coffee, the program
+ for multiple sequence alignment, and sequence
+ formats.
+Section: science
+
+Format: debiandoc-sgml
+Files: /usr/share/doc/t-coffee/t-coffee.sgml.gz
+
+Format: pdf
+Files: /usr/share/doc/t-coffee/t-coffee*.pdf
+
+Format: text
+Files: /usr/share/doc/t-coffee/*.txt.gz
+
+Format: HTML
+Index: /usr/share/doc/t-coffee/html/index.html
+Files: /usr/share/doc/t-coffee/html/*.html
+
+  

Added: trunk/packages/t-coffee/trunk/debian/watch
===================================================================
--- trunk/packages/t-coffee/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/debian/watch	2007-09-24 13:00:29 UTC (rev 451)
@@ -0,0 +1,10 @@
+# Example watch control file for uscan
+# Rename this file to "watch" and then you can run the "uscan" command
+# to check for upstream updates and more.
+# See uscan(1) for format
+
+# Compulsory line, this is a version 2 file
+version=2
+
+# Uncomment to examine a Webserver directory
+http://igs-server.cnrs-mrs.fr/~cnotred/Packages/T-COFFEE_distribution_Version_(.*)\.tar\.gz

Added: trunk/packages/t-coffee/trunk/t_coffee.1
===================================================================
--- trunk/packages/t-coffee/trunk/t_coffee.1	                        (rev 0)
+++ trunk/packages/t-coffee/trunk/t_coffee.1	2007-09-24 13:00:29 UTC (rev 451)
@@ -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/t_coffee_source/makefile
===================================================================
--- trunk/packages/t-coffee/trunk/t_coffee_source/makefile	2007-09-24 13:00:09 UTC (rev 450)
+++ trunk/packages/t-coffee/trunk/t_coffee_source/makefile	2007-09-24 13:00:29 UTC (rev 451)
@@ -1,9 +1,11 @@
 CC=cc
+USER_BIN=../bin
+CFLAGS=-O
 t_coffee: util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o 
-	$(CC)  -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o  -lm
-	mv  t_coffee  ../bin
+	$(CC) -o t_coffee util_constraints_list.o util_job_handling.o util_dps.o util_domain_constraints_list.o util_analyse_constraints_list.o aln_convertion_util.o util_declare.o hsearch.o random.o util_make_tree.o util.o reformat_struc.o reformat.o aln_compare.o io_func.o pb_util_read_sequence.o pb_util_read_seq_util.o tree_util.o util_graph_maln.o util_dp_clean_maln.o util_dp_ssec_pwaln.o util_dp_sim.o util_dp_mm_nw.o util_dp_gotoh_nw.o util_dp_cdna_fasta_nw.o util_dp_generic_fasta_nw.o util_dp_fasta_nw.o util_dp_fasta_sw.o util_dp_gotoh_sw.o util_dp_est.o util_domain_dp_drivers.o util_dp_drivers.o util_domain_dp.o CUSTOM_evaluate_for_struc.o evaluate_for_struc.o evaluate_for_domain.o evaluate_dirichlet.o evaluate.o showpair.o fsa_dp.o pavie_dp.o t_coffee.o  -lm
+	mv  t_coffee  $(USER_BIN)
 
 all:  t_coffee
 
 clean:
-	rm *.o
+	rm -f *.o t_coffee




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