[med-svn] [Git][med-team/theseus][master] 2 commits: Adapt theseus_align to muscle version 5

[Andreas Tille (@tille)]

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 <tille at debian.org>  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 <tille at debian.org>
+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
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