Author: tille Date: 2015-05-21 14:56:11 +0000 (Thu, 21 May 2015) New Revision: 19279
Removed: trunk/packages/theseus/trunk/debian/examples trunk/packages/theseus/trunk/debian/getexamples Modified: trunk/packages/theseus/trunk/debian/changelog trunk/packages/theseus/trunk/debian/control trunk/packages/theseus/trunk/debian/copyright trunk/packages/theseus/trunk/debian/patches/path_to_aligners.patch trunk/packages/theseus/trunk/debian/patches/series trunk/packages/theseus/trunk/debian/rules Log: Split examples into separate binary package; update debian/copyright Modified: trunk/packages/theseus/trunk/debian/changelog =================================================================== --- trunk/packages/theseus/trunk/debian/changelog 2015-05-21 13:39:06 UTC (rev 19278) +++ trunk/packages/theseus/trunk/debian/changelog 2015-05-21 14:56:11 UTC (rev 19279) @@ -1,10 +1,11 @@ -theseus (3.1.1-1) UNRELEASED; urgency=medium +theseus (3.1.1-1) unstable; urgency=medium * New upstream version * cme fix dpkg-control - * Fix PATHes in theseus_align + * Split examples into separate binary package + * update debian/copyright - -- Andreas Tille <[email protected]> Thu, 21 May 2015 14:26:30 +0200 + -- Andreas Tille <[email protected]> Thu, 21 May 2015 16:53:46 +0200 theseus (3.0.0-1) unstable; urgency=medium Modified: trunk/packages/theseus/trunk/debian/control =================================================================== --- trunk/packages/theseus/trunk/debian/control 2015-05-21 13:39:06 UTC (rev 19278) +++ trunk/packages/theseus/trunk/debian/control 2015-05-21 14:56:11 UTC (rev 19279) @@ -15,12 +15,15 @@ Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, - muscle + clustalo Suggests: clustalw, mafft, + muscle, t-coffee, kalign, - dialign + dialign, + probcons, + theseus-examples Description: superimpose macromolecules using maximum likelihood Theseus is a program that simultaneously superimposes multiple macromolecular structures. Theseus finds the optimal solution to the @@ -33,3 +36,22 @@ other programs and algorithms discard residues that are aligned with gaps. Theseus, however, uses a novel superimposition algorithm that includes all of the data. + +Package: theseus-examples +Architecture: all +Depends: ${misc:Depends} +Enhances: theseus +Description: superimpose macromolecules using maximum likelihood (examples) + Theseus is a program that simultaneously superimposes multiple + macromolecular structures. Theseus finds the optimal solution to the + superposition problem using the method of maximum likelihood. By + down-weighting variable regions of the superposition and by correcting for + correlations among atoms, the ML superposition method produces very + accurate structural alignments. + . + When macromolecules with different residue sequences are superimposed, + other programs and algorithms discard residues that are aligned with + gaps. Theseus, however, uses a novel superimposition algorithm that + includes all of the data. + . + This package contains usage examples for theseus. Modified: trunk/packages/theseus/trunk/debian/copyright =================================================================== --- trunk/packages/theseus/trunk/debian/copyright 2015-05-21 13:39:06 UTC (rev 19278) +++ trunk/packages/theseus/trunk/debian/copyright 2015-05-21 14:56:11 UTC (rev 19279) @@ -4,10 +4,10 @@ Source: http://www.theseus3d.org/index.html Files: * -Copyright: © 2003-2012, Douglas L. Theobald -License: GPL3+ +Copyright: © 2003-2015, Douglas L. Theobald +License: GPL-3+ -Files: lbidltmath/ncbi_math.* +Files: libdltmath/ncbi_math.* Copyright: © 1991, Gish, Kans, Ostell and Schuler License: GPL-2+ @@ -63,8 +63,8 @@ Files: debian/* Copyright: © 2007-2008, Morten Kjeldgaard <[email protected]> - © 2008-2012, Andreas Tille <[email protected]> -License: GPL3+ + © 2008-2015, Andreas Tille <[email protected]> +License: GPL-3+ License: GPL-2+ THESEUS is free software; you can redistribute it and/or modify it @@ -84,7 +84,7 @@ On Debian systems, the complete text of the GNU General Public License version 2 can be found in `/usr/share/common-licenses/GPL-2'. -License: GPL3+ +License: GPL-3+ This program 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 3 of the License, or Deleted: trunk/packages/theseus/trunk/debian/examples =================================================================== --- trunk/packages/theseus/trunk/debian/examples 2015-05-21 13:39:06 UTC (rev 19278) +++ trunk/packages/theseus/trunk/debian/examples 2015-05-21 14:56:11 UTC (rev 19279) @@ -1,2 +0,0 @@ -examples/* -debian/getexamples Deleted: trunk/packages/theseus/trunk/debian/getexamples =================================================================== --- trunk/packages/theseus/trunk/debian/getexamples 2015-05-21 13:39:06 UTC (rev 19278) +++ trunk/packages/theseus/trunk/debian/getexamples 2015-05-21 14:56:11 UTC (rev 19279) @@ -1,50 +0,0 @@ -#!/bin/sh -# Get example input files for theseus -# Copyright (C) 2007 Morten Kjeldgaard <[email protected]> -# -# This script 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 2.1 of the License, or (at your option) any later -# version. -# -# This script 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 script; if not, write to the Free -# Software Foundation, Inc., 51 Franklin Street, Fifth Floor, -# Boston, MA 02110-1301 USA -set -e - -pdbs="1s40" - -astrals="d1ciha_ d1crja_ d1csua_ d1csxa_ d1kyow_ d1lfma_ d1m60a_ d1u74d_ d1yeba_ d2pcbb_" -#astrals="d1cih__ d1cih__2 d1crj__ d1csu__ d1csx__ d1kyow_ d1lfma_ d1m60a_ d1u74d_ d1yeb__ d2pcbb_" - -# function to fetch entries from the pdb -pdb_fetch () { - for f in $* ; do - wget -q -O $f.pdb.gz ftp://ftp.wwpdb.org:/pub/pdb/data/structures/all/pdb/pdb${f}.ent.gz - gzip -d ${f}.pdb.gz - echo fetched $f.pdb - done -} - -# function to fetch entries from astral -astral_fetch() { - for f in $* ; do - wget -q -O ${f}.pdb http://astral.berkeley.edu/pdbstyle.cgi?id=${f}&output=text - echo fetched $f.pdb - done -} - -savedir=$PWD -cd /tmp -echo Downloading to directory /tmp -pdb_fetch $pdbs -astral_fetch $astrals - -cd $savedir Modified: trunk/packages/theseus/trunk/debian/patches/path_to_aligners.patch =================================================================== --- trunk/packages/theseus/trunk/debian/patches/path_to_aligners.patch 2015-05-21 13:39:06 UTC (rev 19278) +++ trunk/packages/theseus/trunk/debian/patches/path_to_aligners.patch 2015-05-21 14:56:11 UTC (rev 19279) @@ -4,6 +4,8 @@ Most probably this script wants to be enhanced to select the aligner as an option (rather than editing the script) but that's a suggestion for upstream. +Comment: This patch is actually not activated since it is done in + debian/rules to be save to cope with changed upstream code --- a/theseus_align +++ b/theseus_align Modified: trunk/packages/theseus/trunk/debian/patches/series =================================================================== --- trunk/packages/theseus/trunk/debian/patches/series 2015-05-21 13:39:06 UTC (rev 19278) +++ trunk/packages/theseus/trunk/debian/patches/series 2015-05-21 14:56:11 UTC (rev 19279) @@ -1,2 +1 @@ 30_fix_gcc_options.patch -path_to_aligners.patch Modified: trunk/packages/theseus/trunk/debian/rules =================================================================== --- trunk/packages/theseus/trunk/debian/rules 2015-05-21 13:39:06 UTC (rev 19278) +++ trunk/packages/theseus/trunk/debian/rules 2015-05-21 14:56:11 UTC (rev 19279) @@ -15,5 +15,8 @@ -e 's?/usr/bin/sed?/bin/sed?' \ theseus_align > debian/$(pkg)/usr/bin/theseus_align -override_dh_builddeb: - dh_builddeb -- -Z xz +override_dh_install: + dh_install + # remove macos resource files + find debian -name "._*" -delete + find debian -name ".DS_*" -delete _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
