[med-svn] r19278 - in trunk/packages/theseus/trunk/debian: . patches

[Andreas Tille]

Author: tille
Date: 2015-05-21 13:39:06 +0000 (Thu, 21 May 2015)
New Revision: 19278

Added:
   trunk/packages/theseus/trunk/debian/patches/path_to_aligners.patch
Modified:
   trunk/packages/theseus/trunk/debian/changelog
   trunk/packages/theseus/trunk/debian/patches/series
Log:
Fix PATHes in theseus_align


Modified: trunk/packages/theseus/trunk/debian/changelog
===================================================================
--- trunk/packages/theseus/trunk/debian/changelog	2015-05-21 13:25:20 UTC (rev 19277)
+++ trunk/packages/theseus/trunk/debian/changelog	2015-05-21 13:39:06 UTC (rev 19278)
@@ -1,7 +1,8 @@
-theseus (3.1.1-1) unstable; urgency=medium
+theseus (3.1.1-1) UNRELEASED; urgency=medium
 
   * New upstream version
   * cme fix dpkg-control
+  * Fix PATHes in theseus_align
 
  -- Andreas Tille <tille at debian.org>  Thu, 21 May 2015 14:26:30 +0200
 

Added: trunk/packages/theseus/trunk/debian/patches/path_to_aligners.patch
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/path_to_aligners.patch	                        (rev 0)
+++ trunk/packages/theseus/trunk/debian/patches/path_to_aligners.patch	2015-05-21 13:39:06 UTC (rev 19278)
@@ -0,0 +1,62 @@
+Author: Andreas Tille <tille at debian.org>
+Last-Update: Thu, 21 May 2015 14:26:30 +0200
+Description: Fix PATH to aligners.
+ 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.
+
+--- a/theseus_align
++++ b/theseus_align
+@@ -44,43 +44,43 @@
+ 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";
+ filemapfile="theseus.filemap";
+ 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";
+ 
+ # 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 $align_cmd
+ 
+ # for CLUSTAL-OMEGA -- http://www.clustal.org/omega/
+-alignprog="/usr/local/bin/clustalo";
++alignprog="/usr/bin/clustalo";
+ align_cmd="${alignprog} --force --output-order=input-order -i ${fastafile} -o ${alignmentfile} -v";
+ 
+ 
+ # for CLUSTALW -- http://www.clustal.org/clustal2/
+-#alignprog="/usr/local/bin/clustalw";
++#alignprog="/usr/bin/clustalw";
+ #align_cmd="${alignprog} -outorder=input -infile=${fastafile} -outfile=${alignmentfile}";
+ 
+ # for MAFFT -- http://www.biophys.kyoto-u.ac.jp/%7Ekatoh/programs/align/mafft/
+-# alignprog="/usr/local/bin/mafft";
++# alignprog="/usr/bin/mafft";
+ # align_cmd="${alignprog} --maxiterate 1000 --localpair --clustalout ${fastafile} > ${alignmentfile}";
+ 
+ # for T_COFFEE -- http://igs-server.cnrs-mrs.fr/%7Ecnotred/Projects_home_page/t_coffee_home_page.html
+-#alignprog="/usr/local/bin/t_coffee";
++#alignprog="/usr/bin/t_coffee";
+ #align_cmd="${alignprog} ${fastafile} -outfile=${alignmentfile}";
+ 
+ # for KALIGN -- http://msa.cgb.ki.se/
+-#alignprog="/usr/local/bin/kalign"
++#alignprog="/usr/bin/kalign"
+ #align_cmd="${alignprog} -i ${fastafile} -f aln | sed 's/Kalign/CLUSTALW/' > ${alignmentfile}";
+ 
+ # for DIALIGN2 -- http://bibiserv.techfak.uni-bielefeld.de/dialign/
+-#alignprog="/usr/local/bin/dialign2"
++#alignprog="/usr/bin/dialign2"
+ #align_cmd="${alignprog} -cw ${fastafile}; sed 's/\/\///' ${fastafile%.*}.cw | sed 's/DIALIGN/CLUSTALW/'";
+ 
+ 

Modified: trunk/packages/theseus/trunk/debian/patches/series
===================================================================
--- trunk/packages/theseus/trunk/debian/patches/series	2015-05-21 13:25:20 UTC (rev 19277)
+++ trunk/packages/theseus/trunk/debian/patches/series	2015-05-21 13:39:06 UTC (rev 19278)
@@ -1 +1,2 @@
 30_fix_gcc_options.patch
+path_to_aligners.patch