[med-svn] r19279 - in trunk/packages/theseus/trunk/debian: . patches

Andreas Tille tille at moszumanska.debian.org
Thu May 21 14:56:11 UTC 2015 

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 <tille at debian.org>  Thu, 21 May 2015 14:26:30 +0200
+ -- Andreas Tille <tille at debian.org>  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 <mok at bioxray.au.dk>
-           © 2008-2012, Andreas Tille <tille at debian.org>
-License: GPL3+
+           © 2008-2015, Andreas Tille <tille at debian.org>
+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 <mok at bioxray.dk>
-#
-#  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

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