debian/changelog

-theseus (3.3.0-7) UNRELEASED; urgency=medium
+theseus (3.3.0-7) unstable; urgency=medium
 
   [ Fabian Kloetzl ]
   * Team upload.

debian/patches/path_to_aligners.patch

-Author: Andreas Tille <tille@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.
-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
-@@ -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/'";
- 
-