[med-svn] r5491 - in trunk/packages/theseus/trunk/debian: . patches source

Andreas Tille tille at alioth.debian.org
Wed Nov 24 22:17:08 UTC 2010 

Author: tille
Date: 2010-11-24 22:17:06 +0000 (Wed, 24 Nov 2010)
New Revision: 5491

Added:
   trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch
   trunk/packages/theseus/trunk/debian/source/
   trunk/packages/theseus/trunk/debian/source/format
Modified:
   trunk/packages/theseus/trunk/debian/changelog
   trunk/packages/theseus/trunk/debian/control
   trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch
   trunk/packages/theseus/trunk/debian/patches/series
   trunk/packages/theseus/trunk/debian/theseus_align.1
Log:
Adapt patches to new upstream version; Make sure muscle instead of non-free clustalw will be used as aligner and adjust dependency of muscle accordingly; source format 3


Modified: trunk/packages/theseus/trunk/debian/changelog
===================================================================
--- trunk/packages/theseus/trunk/debian/changelog	2010-11-24 17:02:13 UTC (rev 5490)
+++ trunk/packages/theseus/trunk/debian/changelog	2010-11-24 22:17:06 UTC (rev 5491)
@@ -1,8 +1,15 @@
-theseus (1.5.5-1) UNRELEASED; urgency=low
+theseus (1.5.5-1) unstable; urgency=low
 
   * New upstream version
   * Standards-Version: 3.9.1 (no changes needed)
   * Adapt debian/patches to new upstream version
+  * Source format 3.0 (quilt)
+  * debian/patches/use_muscle_instead_of_clustalw.patch:
+    The script thesaus_align says it would use muscle as align program
+    but it actually uses clustalw which is in non-free and thus we can
+    not recommend it.  The patch makes muscle really the default
+  * Depends: muscle (instead of Suggests)
+  * debian/theseus_align.1: Better wording for muscle preference
 
  -- Andreas Tille <tille at debian.org>  Wed, 24 Nov 2010 17:46:49 +0100
 

Modified: trunk/packages/theseus/trunk/debian/control
===================================================================
--- trunk/packages/theseus/trunk/debian/control	2010-11-24 17:02:13 UTC (rev 5490)
+++ trunk/packages/theseus/trunk/debian/control	2010-11-24 22:17:06 UTC (rev 5491)
@@ -5,7 +5,7 @@
 Uploaders: Morten Kjeldgaard <mok0 at ubuntu.com>,
  Andreas Tille <tille at debian.org>
 DM-Upload-Allowed: yes
-Build-Depends: debhelper (>= 7.1), quilt, libgsl0-dev, liblapack-dev, libtool
+Build-Depends: debhelper (>= 7.1), quilt (>= 0.47), libgsl0-dev, liblapack-dev, libtool
 Standards-Version: 3.9.1
 Homepage: http://www.theseus3d.org
 Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/theseus/trunk/
@@ -13,8 +13,8 @@
 
 Package: theseus
 Architecture: any
-Depends: ${shlibs:Depends}, ${misc:Depends}
-Suggests: muscle, clustlaw, mafft, t-coffee, kalign, dialign
+Depends: ${shlibs:Depends}, ${misc:Depends}, muscle
+Suggests: clustlaw, mafft, t-coffee, kalign, dialign
 Description: superimpose macromolecules using maximum likelihood
  Theseus is a program that simultaneously superimposes multiple
  macromolecular structures. Theseus finds the optimal solution to the

Modified: trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch	2010-11-24 17:02:13 UTC (rev 5490)
+++ trunk/packages/theseus/trunk/debian/patches/10_kbsd.patch	2010-11-24 22:17:06 UTC (rev 5491)
@@ -2,9 +2,9 @@
 Author: Cyril Brulebois <kibi at debian.org>, Andreas Tille <tille at debian.org>
 Fixes: #542879
 
---- theseus.orig/distfit.h
-+++ theseus/distfit.h
-@@ -713,7 +713,7 @@
+--- theseus_src.orig/distfit.h
++++ theseus_src/distfit.h
+@@ -752,7 +752,7 @@
  #ifndef LOGNORMAL_SEEN
  #define LOGNORMAL_SEEN
  
@@ -13,7 +13,7 @@
      extern double erf(double x);
  #endif
  
-@@ -1446,7 +1446,7 @@
+@@ -1485,7 +1485,7 @@
  #ifndef VONMISES_DIST_SEEN
  #define VONMISES_DIST_SEEN
  
@@ -22,8 +22,8 @@
      extern double jn(int n, double x);
  #endif
  
---- theseus.orig/theseus.h
-+++ theseus/theseus.h
+--- theseus_src.orig/theseus.h
++++ theseus_src/theseus.h
 @@ -51,7 +51,7 @@
  #include <string.h>
  #include <stdio.h>

Modified: trunk/packages/theseus/trunk/debian/patches/series
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/series	2010-11-24 17:02:13 UTC (rev 5490)
+++ trunk/packages/theseus/trunk/debian/patches/series	2010-11-24 22:17:06 UTC (rev 5491)
@@ -2,3 +2,4 @@
 200-make.inc.patch
 99-theseus_align.sh.patch
 10_kbsd.patch
+use_muscle_instead_of_clustalw.patch

Added: trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch	                        (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/use_muscle_instead_of_clustalw.patch	2010-11-24 22:17:06 UTC (rev 5491)
@@ -0,0 +1,29 @@
+Description: The script thesaus_align says it would use muscle as align program
+    but it actually uses clustalw which is in non-free and thus we can
+    not recommend it.  The patch makes muscle really the default
+Author: Andreas Tille <tille at debian.org>
+
+--- theseus_src.orig/theseus_align
++++ theseus_src/theseus_align
+@@ -50,8 +50,8 @@
+ alignmentfile="theseus.aln";
+ 
+ # for MUSCLE -- http://www.drive5.com/muscle/
+-#alignprog="/usr/bin/muscle";
+-#align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
++alignprog="/usr/bin/muscle";
++align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
+ 
+ # for PROBCONS -- http://probcons.stanford.edu/
+ #alignprog="/usr/bin/probcons";
+@@ -59,8 +59,8 @@
+ #echo $align_cmd
+ 
+ # for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
+-alignprog="/usr/bin/clustalw";
+-align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}";
++# alignprog="/usr/bin/clustalw";
++# align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}";
+ 
+ # for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/
+ #alignprog="/usr/bin/mafft";

Added: trunk/packages/theseus/trunk/debian/source/format
===================================================================
--- trunk/packages/theseus/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/theseus/trunk/debian/source/format	2010-11-24 22:17:06 UTC (rev 5491)
@@ -0,0 +1 @@
+3.0 (quilt)

Modified: trunk/packages/theseus/trunk/debian/theseus_align.1
===================================================================
--- trunk/packages/theseus/trunk/debian/theseus_align.1	2010-11-24 17:02:13 UTC (rev 5490)
+++ trunk/packages/theseus/trunk/debian/theseus_align.1	2010-11-24 22:17:06 UTC (rev 5491)
@@ -39,12 +39,11 @@
 that you supply.
 .P
 Second, these sequences are aligned using the multiple sequence alignment
-program of your choice. The script is easily modified for CLUSTALW,
+program of your choice. The script can easily be modified for CLUSTALW,
 T_COFFEE, KALIGN, DIALIGN2, or MAFFT. Any multiple sequence alignment
 program can be used, as long as it can generate clustal-formatted
 files. However, I highly recommend Bob Edgar's MUSCLE program for both its
-speed and accuracy. It is easy to install using either precompiled binaries
-or by compiling from scratch: http://www.drive5.com/muscle/
+speed and accuracy. (For more info see http://www.drive5.com/muscle/ .)
 .P
 Third, \fBtheseus\fR performs a superposition of the structures using the
 sequence alignment as a guide.

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