--- t-coffee-8.14.orig/debian/README.Debian +++ t-coffee-8.14/debian/README.Debian @@ -0,0 +1,43 @@ +T-COFFEE for Debian +------------------- + +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. + +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). + +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 + +and/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 + +and/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 + +and/or + + 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. --- t-coffee-8.14.orig/debian/changelog +++ t-coffee-8.14/debian/changelog @@ -0,0 +1,91 @@ +t-coffee (8.14-1) unstable; urgency=low + + * New upstream version + + -- Andreas Tille Tue, 03 Nov 2009 13:56:33 +0100 + +t-coffee (8.13-1) unstable; urgency=low + + * New upstream version + + -- Andreas Tille Thu, 01 Oct 2009 22:13:34 +0200 + +t-coffee (8.06-1) unstable; urgency=low + + [ Charles Plessy ] + TODO: + Identify differences and document relevant ones. + Check that the patch can be dropped. + Support PDB in getdata. + Get the FORTRAN building right. + NOTE + The upstream install system was completely refactored, and T-Coffee + includes new functionalities that require internet access. We have to + understand them before updating our package. + + * New upstream release + - say something about libsoap-lite-perl ? + * debian/control: + - t-coffee recommends libsoap-lite-perl. + - Added missing comma in t-coffee Suggests field (Closes:#536956). + + [ Andreas Tille ] + * debian/control: + - Standards-Version: 3.8.3 (added README.source) + - Added myself to uploaders + - s/Debian-Med/Debian Med/ + - Bumped debhelper version to >= 7.1 to possibly enable short + rules files. + - Added "Depends: ${misc:Depends}" to all packages + + -- Andreas Tille Fri, 25 Sep 2009 14:41:41 +0200 + +t-coffee (5.72-1) unstable; urgency=low + + [ David Paleino ] + * New upstream release + + [ Charles Plessy ] + * Switched to CDBS. + * debian/patches: + - Upated the dm-coffee patch because dialign-t was renamed dialign-tx. + - Dropped the unicode conversion patch. + - Dropped the manpage patch (implements the clear rule through CDBS). + * Updated my email address. + + -- Charles Plessy Mon, 30 Jun 2008 23:34:32 +0900 + +t-coffee (5.31-1) unstable; urgency=low + + * New upstream version. + * Debian menu transition: updated debian/t-coffee-doc.doc-base. + * debian/patches/dmcoffee.patch: to make dmcoffee work + out of the box. + * debian/control: + - Allowed Debian Maintainers to upload t-coffee. + - Checked that the package conforms to Policy 3.7.3. + - Using debhelper 5. + - Updated homepage. + - Moved t-coffee-doc to section doc. + * debian/copyright: converted to machine-readable format. + * debian/rules: builds only indep or only arch when called with + binary-indep or binary-arch (Closes: #457921). + + -- Charles Plessy Sat, 29 Dec 2007 18:54:09 +0100 + +t-coffee (5.05-1) unstable; urgency=low + + * New upstream version. + * Assigned maintainership to Debian-Med. + * Moved boxshade from Recommended to Suggested. + * Added use of quilt. + * Homepage received its separate line. + + -- Steffen Moeller Mon, 24 Sep 2007 15:05:07 +0200 + +t-coffee (2.50-1) unstable; urgency=low + + * Initial Release (Closes: Bug#205370). + + -- Steffen Moeller Fri, 13 May 2005 10:52:14 +0200 + --- t-coffee-8.14.orig/debian/compat +++ t-coffee-8.14/debian/compat @@ -0,0 +1 @@ +5 --- t-coffee-8.14.orig/debian/control +++ t-coffee-8.14/debian/control @@ -0,0 +1,57 @@ +Source: t-coffee +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team +DM-Upload-Allowed: yes +Uploaders: Steffen Moeller , + Charles Plessy , + Andreas Tille +Build-Depends: debhelper (>= 7.1), cdbs, quilt +Standards-Version: 3.8.3 +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} +Recommends: libsoap-lite-perl +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 +Depends: ${misc:Depends} +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 +Depends: ${misc:Depends} +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. --- t-coffee-8.14.orig/debian/copyright +++ t-coffee-8.14/debian/copyright @@ -0,0 +1,32 @@ +Format-Specification: http://wiki.debian.org/Proposals/CopyrightFormat?action=recall&rev=129 +Upstream-Author: Cédric Notredame +Packaged-By: Steffen Moeller +Packaged-Date: Fri, 13 May 2005 10:52:14 +0200 +Original-Source-Location: http://www.tcoffee.org/Packages/T-COFFEE_distribution_Version_7.54.tar.gz + +Files: * +Copyright: Centre National de la Recherche Scientifique (CNRS) + Cédric Notredame +License: GPL-2+ + T-COFFEE 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. + . + 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 +X-Comment: On Debian systems, the complete text of the GNU General + Public License can be found in `/usr/share/common-licenses/GPL'. + +Files: debian/* +Copyright: © 2005-2007 Steffen Möller +License: unknown +Copyright: © 2006-2009 Charles Plessy + © 2008 David Paleino +License: same as T-Coffee itself --- t-coffee-8.14.orig/debian/rules +++ t-coffee-8.14/debian/rules @@ -0,0 +1,14 @@ +#!/usr/bin/make -f + +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 + +# DEB_SRCDIR = t_coffee_source +# Is messing with /usr/share/cdbs/1/rules/patchsys-quilt.mk + +DEB_MAKE_BUILD_TARGET = -C t_coffee_source -i USER_BIN=../bin/ all + +clean:: + dh_clean t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee $(shell find example/ -size 0) + chmod 644 example/* --- t-coffee-8.14.orig/debian/t-coffee-doc.docs +++ t-coffee-8.14/debian/t-coffee-doc.docs @@ -0,0 +1 @@ +doc/* --- t-coffee-8.14.orig/debian/t-coffee-examples.docs +++ t-coffee-8.14/debian/t-coffee-examples.docs @@ -0,0 +1 @@ +example/* --- t-coffee-8.14.orig/debian/t-coffee.install +++ t-coffee-8.14/debian/t-coffee.install @@ -0,0 +1 @@ +t_coffee_source/t_coffee /usr/bin --- t-coffee-8.14.orig/debian/watch +++ t-coffee-8.14/debian/watch @@ -0,0 +1,2 @@ +version=3 +http://www.tcoffee.org/Packages/ T-COFFEE_distribution_Version_(.*)\.tar\.gz --- t-coffee-8.14.orig/debian/t-coffee.manpages +++ t-coffee-8.14/debian/t-coffee.manpages @@ -0,0 +1 @@ +debian/t_coffee.1 --- t-coffee-8.14.orig/debian/t_coffee.1 +++ t-coffee-8.14/debian/t_coffee.1 @@ -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 +.PP +This manual page was written by Steffen Moeller , +for the Debian project (but may be used by others). --- t-coffee-8.14.orig/debian/t-coffee-doc.doc-base.technical +++ t-coffee-8.14/debian/t-coffee-doc.doc-base.technical @@ -0,0 +1,13 @@ +Document: t-coffee-technical +Title: T-Coffee: Technical documentation +Author: Cédric Notredame +Abstract: This manual describes the installation of T-Coffee + and provides a reference manual for all its options. +Section: Science/Biology + +Format: Text +Files: /usr/share/doc/t-coffee-doc/t_coffee_technical.txt.gz + +Format: HTML +Index: /usr/share/doc/t-coffee-doc/t_coffee_technical.htm +Files: /usr/share/doc/t-coffee-doc/t_coffee_technical.htm --- t-coffee-8.14.orig/debian/t-coffee-doc.doc-base.tutorial +++ t-coffee-8.14/debian/t-coffee-doc.doc-base.tutorial @@ -0,0 +1,17 @@ +Document: t-coffee-tutorial +Title: T-Coffee: Tutorial and FAQ +Author: Cédric Notredame +Abstract: This Document contains two main sections. + The first one is a tutorial, where we go from simple things to more + complicated and show you how to use all the subtleties of T-Coffee. We have + tried to put as many of these functionalities on the web (www.tcoffee.org) but + if you need to do something special and highly reproducible, the Command Line + is the only way. +Section: Science/Biology + +Format: Text +Files: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.txt.gz + +Format: HTML +Index: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.htm +Files: /usr/share/doc/t-coffee-doc/t_coffee_tutorial.htm --- t-coffee-8.14.orig/debian/README.source +++ t-coffee-8.14/debian/README.source @@ -0,0 +1,4 @@ +This packages uses the quilt patch system. Please read +/usr/share/doc/quilt/README.source for more information. + + -- Andreas Tille Fri, 25 Sep 2009 14:41:41 +0200 --- t-coffee-8.14.orig/debian/patches/dmcoffee.patch +++ t-coffee-8.14/debian/patches/dmcoffee.patch @@ -0,0 +1,71 @@ +Author: Charles Plessy +Forwarded: Cédric Notredame +Description: To make (D)M-COFFEE work out of the box on Debian. + The path to dialign-tx and to the blosum matrix of POA are hardcoded + through this patch, so that (D)M-COFFEE work without manual copying + and/or linking. +License: Same as T-COFFEE itself. +--- a/t_coffee_source/util_constraints_list.c ++++ b/t_coffee_source/util_constraints_list.c +@@ -1397,13 +1397,13 @@ + 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-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"); +@@ -1416,12 +1416,12 @@ + 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-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"); +@@ -1443,7 +1443,7 @@ + fprintf ( fp, "PARAM1 -toupper \n"); + fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n"); + fprintf ( fp, "OUT_FLAG -clustal&bnsp\n"); +- fprintf ( fp, "PARAM %s/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee()); ++ fprintf ( fp, "PARAM /usr/share/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee()); + fprintf ( fp, "SEQ_TYPE S\n"); + + vfclose (fp); +@@ -1461,7 +1461,7 @@ + fprintf ( fp, "PARAM1 -toupper \n"); + fprintf ( fp, "IN_FLAG -read_fasta&bnsp\n"); + fprintf ( fp, "OUT_FLAG -clustal&bnsp\n"); +- fprintf ( fp, "PARAM %s/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee()); ++ fprintf ( fp, "PARAM /usr/share/poa/blosum80.mat&bnsp2>/dev/null\n", get_mcoffee_4_tcoffee()); + fprintf ( fp, "SEQ_TYPE S\n"); + + vfclose (fp); +--- a/t_coffee_source/define_header.h ++++ b/t_coffee_source/define_header.h +@@ -331,8 +331,8 @@ + #define CLUSTALW_4_TCOFFEE "clustalw" + #define POA_4_TCOFFEE "poa" + #define PROBCONS_4_TCOFFEE "probcons" +-#define PROBCONSRNA_4_TCOFFEE "probconsRNA" +-#define DIALIGNT_4_TCOFFEE "dialign-t" ++#define PROBCONSRNA_4_TCOFFEE "probcons-RNA" ++#define DIALIGNT_4_TCOFFEE "dialign-tx" + #define MAFFT_4_TCOFFEE "mafft" + #define MUSCLE_4_TCOFFEE "muscle" + #define TCOFFEE_4_TCOFFEE "t_coffee" --- t-coffee-8.14.orig/debian/patches/series +++ t-coffee-8.14/debian/patches/series @@ -0,0 +1 @@ +#dmcoffee.patch