[med-svn] r5490 - in trunk/packages/theseus/trunk/debian: . patches
Andreas Tille
tille at alioth.debian.org
Wed Nov 24 17:02:18 UTC 2010
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";
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