Andreas Tille pushed to branch master at Debian Med / theseus
Commits: c46f689c by Andreas Tille at 2018-09-10T13:43:57Z Remove unused patch - - - - - 8b1a4a5d by Andreas Tille at 2018-09-10T13:47:23Z Upload to unstable - - - - - 2 changed files: - debian/changelog - − debian/patches/path_to_aligners.patch Changes: ===================================== debian/changelog ===================================== @@ -1,4 +1,4 @@ -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 deleted ===================================== @@ -1,64 +0,0 @@ -Author: Andreas Tille <[email protected]> -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/'"; - - View it on GitLab: https://salsa.debian.org/med-team/theseus/compare/f090a181124b83eb21d33ea646203f9b3b39e877...8b1a4a5d4a3ecc66f8c9d31a56a573c2f3c8f441 -- View it on GitLab: https://salsa.debian.org/med-team/theseus/compare/f090a181124b83eb21d33ea646203f9b3b39e877...8b1a4a5d4a3ecc66f8c9d31a56a573c2f3c8f441 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] https://alioth-lists.debian.net/cgi-bin/mailman/listinfo/debian-med-commit
