debian/0000755000000000000000000000000012245364575007203 5ustar debian/README.source0000644000000000000000000000026711257135633011360 0ustar 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 debian/rules0000755000000000000000000000140312015206244010240 0ustar #!/usr/bin/make -f # DEB_SRCDIR = t_coffee_source # Is messing with /usr/share/cdbs/1/rules/patchsys-quilt.mk FCC = gfortran $(shell dpkg-buildflags --get FFLAGS) %: dh $@ --sourcedirectory=t_coffee_source override_dh_auto_build: dh_auto_build -- -i USER_BIN=../bin/ FCC="$(FCC)" all override_dh_auto_clean: rm -rf t_coffee_source/*.o t_coffee_source/t_coffee bin/t_coffee $(shell find example/ -size 0) bin/t_coffee rm -rf t_coffee_source/TMalign chmod 644 example/* override_dh_compress: #Compressing most of the files in examples/ makes them unusable dh_compress -Xt-coffee-examples ( cd debian/t-coffee-examples/ && \ chmod 644 usr/share/doc/t-coffee-examples/changelog.Debian && \ gzip -9 usr/share/doc/t-coffee-examples/changelog.Debian ) || true debian/patches/0000755000000000000000000000000012245363653010626 5ustar debian/patches/probconsrna.patch0000644000000000000000000000111212244551044014160 0ustar Description: Debian-specific adjustment. The program "probconsRNA" is called "probcons-RNA" in Debian. Forwarded: not-needed --- a/t_coffee_source/programmes_define.h +++ b/t_coffee_source/programmes_define.h @@ -250,7 +250,7 @@ #define DALILITEc_source "empty" #define DALILITEc_update_action "never" #define DALILITEc_mode "expresso,3dcoffee" -#define PROBCONSRNA_4_TCOFFEE "probconsRNA" +#define PROBCONSRNA_4_TCOFFEE "probcons-RNA" #define PROBCONSRNA_type "RNA_multiple_aligner" #define PROBCONSRNA_ADDRESS "http://probcons.stanford.edu/" #define PROBCONSRNA_language "C++" debian/patches/series0000644000000000000000000000002211521300167012020 0ustar probconsrna.patch debian/source/0000755000000000000000000000000012245363653010477 5ustar debian/source/format0000644000000000000000000000001411357700135011676 0ustar 3.0 (quilt) debian/t-coffee.manpages0000644000000000000000000000002210777141606012376 0ustar debian/t_coffee.1 debian/copyright0000644000000000000000000000313712244551044011126 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_10.00.r1613.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 Comment: On Debian systems, the complete text of the GNU General Public License version 2 can be found in ‘/usr/share/common-licenses/GPL-2’. Files: debian/* Copyright: © 2005-2007 Steffen Möller © 2006-2009 Charles Plessy © 2008 David Paleino License: unknown Contributions of Charles Plessy and David Paleino are licensed under the same terms as T-Coffee itself. Redistribution terms for earlier contributions are unknown. Later contributions are expected to be also under the same terms as T-Coffee itself. debian/t-coffee-examples.docs0000644000000000000000000000001210700050112013317 0ustar example/* debian/watch0000644000000000000000000000015111521300167010210 0ustar version=3 http://www.tcoffee.org/Packages/Stable/Latest/T-COFFEE_distribution_Version_([^_]*).*\.tar\.gz debian/changelog0000644000000000000000000001411312245363606011047 0ustar t-coffee (10.00.r1613-1) unstable; urgency=low * New upstream release. -- Charles Plessy Wed, 27 Nov 2013 21:37:22 +0900 t-coffee (9.03.r1318-1) unstable; urgency=low * New upstream release. [ Tim Booth ] * Removed the -doc package as it is empty (Closes: #688630). docs are no longer in tarball but online: http://www.tcoffee.org/Projects/tcoffee/#DOCUMENTATION * Rejigged the rules file to use DH, not CDBS. * Avoid compressing files under t-coffee-examples * Remove TMalign binary on clean (should avoid building it at all) * Fix minor typo flagged by Lintian [ Charles Plessy ] * Normalised debian/control with config-model-edit. * Normalised VCS URLs. * Using Debhelper 9. * Complies with Policy 3.9.4. [Andreas Tille] * debian/upstream: Single Reference field instead of Reference-* -- Charles Plessy Sun, 14 Jul 2013 19:03:20 +0900 t-coffee (9.02.r1228-2) unstable; urgency=low * Recommend tm-align instead of distributing local copy (debian/control, debian/t-coffee.install, Closes: #661516). -- Charles Plessy Fri, 02 Mar 2012 14:04:20 +0900 t-coffee (9.02.r1228-1) unstable; urgency=low * New upstream release (Closes: #649263). * Build new Fortran tool (debian/rules debian/contol debian/t-coffee.install) * Corrected debian/rules as upstream test suite was removed. * Complies with Policy 3.9.3 (debian/control, no other changes needed). * Removed doc-base registrations debian/t-coffee-doc.doc-base.technical and debian/t-coffee-doc.doc-base.tutorial, as the files disappeared upstream. -- Charles Plessy Mon, 27 Feb 2012 13:09:36 +0900 t-coffee (8.99-1) unstable; urgency=low * New upstream release in Debian. * Converted and validated debian/copyright to DEP 5 machine-readable format. * Using debhelper 8 (debian/control, debian/compat). * Incremented Standards-Version to reflect conformance with Policy 3.9.2. (debian/control, no change needed). * Corrected VCS URLs in debian/control. * Run upstream tests at build time (debian/rules, debian/README.test). -- Charles Plessy Tue, 21 Jun 2011 14:14:10 +0900 t-coffee (8.99-0ubuntu1) lucid; urgency=low * Rebuild for new upstream release. * There is no changelog from upstream to read. -- Tim Booth Sat, 29 Jan 2011 15:18:01 +0000 t-coffee (8.97-0ubuntu2) lucid; urgency=low * New upstream release, changed watch file and auto rebuild using uupdate * Cleared out old patch - apparently unneeded or else needs total re-write -- Tim Booth Tue, 23 Nov 2010 14:01:22 +0000 t-coffee (8.95-1) lucid; urgency=low * New upstream version, rebuild by Tim for Bio-Linux/Lucid -- Tim Booth Mon, 01 Nov 2010 15:05:07 +0000 t-coffee (8.84-1) unstable; urgency=low * New upstream version -- Andreas Tille Thu, 24 Jun 2010 14:46:16 +0200 t-coffee (8.47-1) unstable; urgency=low [ Charles Plessy ] * Collected Upstream information in debian/upstream-metadata.yaml. [ Andreas Tille ] * New upstream version * Source format 3.0 (quilt) * Standards-Version: 3.8.4 (no changes needed) -- Andreas Tille Fri, 09 Apr 2010 21:08:32 +0200 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 debian/upstream0000644000000000000000000000126711725761435010772 0ustar Contact: Cédric Notredame Name: T-Coffee Homepage: http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html Reference: DOI: 10.1006/jmbi.2000.4042 PMID: 10964570 Author: Cédric Notredame and Desmond G. Higgins and Jaap Heringa Journal: Journal of Molecular Biology Number: 1 Pages: 205-217 Title: > T-coffee: a novel method for fast and accurate multiple sequence alignment URL: http://www.sciencedirect.com/science/article/B6WK7-45F5150-7S/2/9c2fd0f2a43f877fd801b3245fe0beed Volume: 302 Year: 2000 Watch: http://www.tcoffee.org/Packages/ T-COFFEE_distribution_Version_(.*)\.tar\.gz Webservice: http://tcoffee.crg.cat/apps/tcoffee/do:regular debian/t-coffee.install0000644000000000000000000000004211724054602012243 0ustar t_coffee_source/t_coffee /usr/bin debian/control0000644000000000000000000000442212244551231010572 0ustar Source: t-coffee Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Charles Plessy , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), gfortran Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/t-coffee/trunk/ Vcs-Svn: svn://anonscm.debian.org/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, libxml-simple-perl, tm-align Suggests: boxshade, seaview, t-coffee-examples, dialign-tx, kalign, mafft, muscle, poa, probcons, clustalw, amap-align, proda 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 can also 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 Depends: ${misc:Depends} Recommends: t-coffee Description: annotated examples for the use of T-Coffee To help increasing the proficiency in the use of T-Coffee, this package provides examples for input sequences and their proper alignment. debian/README.Debian0000644000000000000000000000332010777141606011236 0ustar T-COFFEE for Debian ------------------- T-COFFEE comes with a special mode, M-COFFEE, that makes it possible to combine the output of many multiple sequence alignment packages. In its published version, it uses MUSCLE, PROBCONS, POA, DiAlign-T, MAFFT, Clustal W, PCMA and T-Coffee. A special version has been made for Debian, DM-Coffee, that uses only free software by replacing Clustal W by Kalign. Using the 8 Methods of M-Coffee can sometimes be a bit heavy. You can use a subset of your favorite methods if you prefer. This version of T-COFFEE has been patched to use the latest program of the DiAlign family, DiAlign-TX. To install all the necessary programs for running DM-COFFEE, you can run use the option `~Rsuggests:^package$' 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. debian/compat0000644000000000000000000000000212170470532010365 0ustar 9 debian/t_coffee.10000644000000000000000000001211610777141606011034 0ustar .\" 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).