Andreas Tille pushed to branch master at Debian Med / theseus
Commits: 1c2de261 by Andreas Tille at 2022-01-30T17:08:27+01:00 Adapt theseus_align to muscle version 5 - - - - - db477b8d by Andreas Tille at 2022-01-30T17:22:02+01:00 routine-update: Ready to upload to unstable - - - - - 3 changed files: - debian/changelog - + debian/patches/adapt_to_muscle5.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +theseus (3.3.0-11) unstable; urgency=medium + + * Adapt theseus_align to muscle version 5 + Closes: #1004506 + + -- Andreas Tille <[email protected]> Sun, 30 Jan 2022 17:18:29 +0100 + theseus (3.3.0-10) unstable; urgency=medium * Fix watch file ===================================== debian/patches/adapt_to_muscle5.patch ===================================== @@ -0,0 +1,27 @@ +Description: Adapt theseus_align to muscle version 5 +Bug-Debian: https://bugs.debian.org/1004506 +Author: Andreas Tille <[email protected]> +Last-Update: Sun, 30 Jan 2022 08:41:43 +0100 + +--- a/theseus_align ++++ b/theseus_align +@@ -50,8 +50,8 @@ filemapfile="theseus.filemap"; + alignmentfile="theseus.aln"; + + # for MUSCLE -- http://www.drive5.com/muscle/ +-alignprog="/usr/local/bin/muscle"; +-align_cmd="${alignprog} -maxiters 32 -in ${fastafile} -out ${alignmentfile} -clwstrict"; ++alignprog="/usr/bin/muscle"; ++align_cmd="${alignprog} -align ${fastafile} -output ${alignmentfile}"; + + # for PROBCONS -- http://probcons.stanford.edu/ + # alignprog="/usr/local/bin/probcons"; +@@ -64,7 +64,7 @@ align_cmd="${alignprog} -maxiters 32 -in + + + # 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/ ===================================== debian/patches/series ===================================== @@ -3,3 +3,4 @@ gcc-7.patch 0003-fix-issues-uncovered-by-gcc8.patch 0004-create-lib-dir.patch 0005_stringbuffer.patch +adapt_to_muscle5.patch View it on GitLab: https://salsa.debian.org/med-team/theseus/-/compare/57c0ae6aaf084d9fcc3d53c0c61c5e91ac395850...db477b8da277380d1840d3bf844ff48dae9d251c -- View it on GitLab: https://salsa.debian.org/med-team/theseus/-/compare/57c0ae6aaf084d9fcc3d53c0c61c5e91ac395850...db477b8da277380d1840d3bf844ff48dae9d251c You're receiving this email because of your account on salsa.debian.org.
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