[med-svn] [Git][med-team/seaview][master] Patch for command-line arguments of MUSCLE 5.

[Charles Plessy (@plessy)]

Charles Plessy pushed to branch master at Debian Med / seaview


Commits:
15722bf4 by Charles Plessy at 2022-12-15T15:14:40+09:00
Patch for command-line arguments of MUSCLE 5.

- - - - -


4 changed files:

- align.cxx
- debian/changelog
- + debian/patches/muscle5
- + debian/patches/series


Changes:

=====================================
align.cxx
=====================================
@@ -1012,7 +1012,7 @@ void init_msa_algos(void)
   set_res_value("msa_name_1", "clustalo"); 
   set_res_value("msa_args_1", "-v -i %f.pir -o %f.out --outfmt=fasta");
   set_res_value("msa_name_2", "muscle"); 
-  set_res_value("msa_args_2", "-in %f.pir -out %f.out");
+  set_res_value("msa_args_2", "-align %f.pir -output %f.out");
   if (count < 2) {
     set_res_value("msa_algo_count", "2");
     set_res_value("alignment", "0"); /* clustal-omega is default starting msa method */


=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+seaview (1:5.0.5-2) unstable; urgency=medium
+
+  * Patch for command-line arguments of MUSCLE 5.
+
+ -- Charles Plessy <plessy at debian.org>  Thu, 15 Dec 2022 15:09:37 +0900
+
 seaview (1:5.0.5-1) unstable; urgency=medium
 
   * New upstream version


=====================================
debian/patches/muscle5
=====================================
@@ -0,0 +1,26 @@
+Description: Adapt to new command-line arguments in MUSCLE 5
+ The muscle package now ships version 5 of the program, which is a complete
+ re-implementation and is not backwards-compatible.  This patch updates
+ the command-line arguments passed to muscle.
+Author: Charles Plessy <plessy at debian.org>
+
+---
+The information above should follow the Patch Tagging Guidelines, please
+checkout https://dep.debian.net/deps/dep3/ to learn about the format. Here
+are templates for supplementary fields that you might want to add:
+
+Origin: vendor
+Forwarded: no
+Last-Update: 2022-12-15
+
+--- seaview-5.0.5.orig/align.cxx
++++ seaview-5.0.5/align.cxx
+@@ -1012,7 +1012,7 @@ void init_msa_algos(void)
+   set_res_value("msa_name_1", "clustalo"); 
+   set_res_value("msa_args_1", "-v -i %f.pir -o %f.out --outfmt=fasta");
+   set_res_value("msa_name_2", "muscle"); 
+-  set_res_value("msa_args_2", "-in %f.pir -out %f.out");
++  set_res_value("msa_args_2", "-align %f.pir -output %f.out");
+   if (count < 2) {
+     set_res_value("msa_algo_count", "2");
+     set_res_value("alignment", "0"); /* clustal-omega is default starting msa method */


=====================================
debian/patches/series
=====================================
@@ -0,0 +1 @@
+muscle5



View it on GitLab: https://salsa.debian.org/med-team/seaview/-/commit/15722bf490e433a39daa78de150020df02380b95

-- 
View it on GitLab: https://salsa.debian.org/med-team/seaview/-/commit/15722bf490e433a39daa78de150020df02380b95
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