[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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