[med-svn] r5490 - in trunk/packages/theseus/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2010-11-24 17:02:13 +0000 (Wed, 24 Nov 2010)
New Revision: 5490

Modified:
   trunk/packages/theseus/trunk/debian/changelog
   trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch
Log:
Adapt patch to new upstream version


Modified: trunk/packages/theseus/trunk/debian/changelog
===================================================================
--- trunk/packages/theseus/trunk/debian/changelog	2010-11-24 16:58:10 UTC (rev 5489)
+++ trunk/packages/theseus/trunk/debian/changelog	2010-11-24 17:02:13 UTC (rev 5490)
@@ -2,7 +2,7 @@
 
   * New upstream version
   * Standards-Version: 3.9.1 (no changes needed)
-  * Adapt debian/patches/200-make.inc.patch to new upstream version
+  * Adapt debian/patches to new upstream version
 
  -- Andreas Tille <tille at debian.org>  Wed, 24 Nov 2010 17:46:49 +0100
 

Modified: trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch	2010-11-24 16:58:10 UTC (rev 5489)
+++ trunk/packages/theseus/trunk/debian/patches/99-theseus_align.sh.patch	2010-11-24 17:02:13 UTC (rev 5490)
@@ -2,12 +2,12 @@
 ANTENTION: This patch is currently not used
 Authors: Morten Kjeldgaard <mok at bioxray.dk>, Andreas Tille <tille at debian.org>
 
---- theseus.orig/theseus_align
-+++ theseus/theseus_align
-@@ -41,33 +41,33 @@
- # The following six constant strings should be modified to whatever is
- # convenient and applicable.
- 
+--- theseus_src.orig/theseus_align
++++ theseus_src/theseus_align
+@@ -44,38 +44,38 @@
+ CAT="/bin/cat";
+ SED="/usr/bin/sed";
+ TEE="/usr/bin/tee";
 -theseus="/usr/local/bin/theseus"; # where to find the THESEUS binary executable
 +theseus="/usr/bin/theseus"; # where to find the THESEUS binary executable
  fastafile="theseus.fasta";
@@ -15,14 +15,20 @@
  alignmentfile="theseus.aln";
  
  # for MUSCLE -- http://www.drive5.com/muscle/
--alignprog="/usr/local/bin/muscle";
-+alignprog="/usr/bin/muscle";
- align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
+-#alignprog="/usr/local/bin/muscle";
++#alignprog="/usr/bin/muscle";
+ #align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict";
  
+ # for PROBCONS -- http://probcons.stanford.edu/
+-#alignprog="/usr/local/bin/probcons";
++#alignprog="/usr/bin/probcons";
+ #align_cmd="( ${alignprog} -clustalw ${fastafile} | ${SED} 's/PROBCONS/CLUSTALW/' | ${TEE} ${alignmentfile} )";
+ #echo $align_cmd
+ 
  # for CLUSTALW -- ftp://ftp-igbmc.u-strasbg.fr/pub/ClustalW/
--#alignprog="/usr/local/bin/clustlaw";
-+#alignprog="/usr/bin/clustlaw";
- #align_cmd="${alignprog} -infile=${fastafile} -outfile=${alignmentfile}";
+-alignprog="/usr/local/bin/clustalw";
++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/local/bin/mafft";