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 <[email protected]> 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 <[email protected]>, Andreas Tille <[email protected]> ---- 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"; _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
