[med-svn] [Git][med-team/bioperl-run][master] 6 commits: update-kalign-invocation.patch: new.

[Étienne Mollier (@emollier)]

Étienne Mollier pushed to branch master at Debian Med / bioperl-run


Commits:
0825ac48 by Étienne Mollier at 2026-03-09T20:21:08+01:00
update-kalign-invocation.patch: new.

This change adjusts arguments passed to kalign to use stdin as input
and stdout as output, per the new command version's usage
instructions.

Closes: #1129866

- - - - -
690528e2 by Étienne Mollier at 2026-03-09T20:22:34+01:00
d/control: drop redundant Priority: optional.

- - - - -
9aec1a0f by Étienne Mollier at 2026-03-09T20:22:51+01:00
d/control: drop redundant Rules-Requires-Root: no.

- - - - -
bcae4c59 by Étienne Mollier at 2026-03-09T20:23:29+01:00
d/control: declare compliance to standards version 4.7.3.

- - - - -
61ce3328 by Étienne Mollier at 2026-03-09T20:42:47+01:00
d/watch: rework to port to Github uscan template.

- - - - -
b5ffc81a by Étienne Mollier at 2026-03-09T20:43:55+01:00
d/changelog: ready for upload to unstable.

- - - - -


5 changed files:

- debian/changelog
- debian/control
- debian/patches/series
- + debian/patches/update-kalign-invocation.patch
- debian/watch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,16 @@
+bioperl-run (1.7.3-14) unstable; urgency=medium
+
+  * update-kalign-invocation.patch: new.
+    This change adjusts arguments passed to kalign to use stdin as input
+    and stdout as output, per the new command version's usage
+    instructions. (Closes: #1129866)
+  * d/control: drop redundant Priority: optional.
+  * d/control: drop redundant Rules-Requires-Root: no.
+  * d/control: declare compliance to standards version 4.7.3.
+  * d/watch: rework to port to Github uscan template.
+
+ -- Étienne Mollier <emollier at debian.org>  Mon, 09 Mar 2026 20:43:42 +0100
+
 bioperl-run (1.7.3-13) unstable; urgency=medium
 
   * Revert "skip_tests_for_ncbi-blast+.patch: remove."


=====================================
debian/control
=====================================
@@ -5,7 +5,6 @@ Uploaders: Charles Plessy <plessy at debian.org>,
            Étienne Mollier <emollier at debian.org>
 Section: science
 Testsuite: autopkgtest-pkg-perl
-Priority: optional
 Build-Depends: debhelper-compat (= 13), libmodule-build-perl
 Build-Depends-Indep: perl,
                      bioperl (>= 1.7.4),
@@ -61,11 +60,10 @@ Build-Depends-Indep: perl,
                      pftools [any-amd64],
 # Needed for the network tests:
                      libwww-perl
-Standards-Version: 4.7.0
+Standards-Version: 4.7.3
 Vcs-Browser: https://salsa.debian.org/med-team/bioperl-run
 Vcs-Git: https://salsa.debian.org/med-team/bioperl-run.git
 Homepage: https://metacpan.org/release/BioPerl-Run
-Rules-Requires-Root: no
 
 Package: bioperl-run
 Architecture: all


=====================================
debian/patches/series
=====================================
@@ -19,3 +19,4 @@ unscramble-erpin.patch
 fix-pod-conversion.patch
 adjust-muscle-test.patch
 update-blastdbcmd-error-output.patch
+update-kalign-invocation.patch


=====================================
debian/patches/update-kalign-invocation.patch
=====================================
@@ -0,0 +1,18 @@
+Description: update kalign invocation arguments.
+Author: Étienne Mollier <emollier at debian.org>
+Bug-Debian: https://bugs.debian.org/1129866
+Forwarded: no
+Last-Update: 2026-03-09
+---
+This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
+--- bioperl-run.orig/lib/Bio/Tools/Run/Alignment/Kalign.pm
++++ bioperl-run/lib/Bio/Tools/Run/Alignment/Kalign.pm
+@@ -464,7 +464,7 @@
+ 	undef $tfh;
+ 	$self->outfile_name($outfile);
+     }
+-    $param_string .= " -out ".$self->outfile_name;
++    $param_string .= " -i - -o ".$self->outfile_name;
+     
+     if ($self->quiet() || $self->verbose < 0) {
+ 	my $null = ($^O =~ m/mswin/i) ? 'NUL' : '/dev/null';


=====================================
debian/watch
=====================================
@@ -1,5 +1,7 @@
-version=4
-opts="uversionmangle=s/^release-\(.*\)$/\1/;s/[-_]/./g,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
-	https://github.com/bioperl/bioperl-run/tags (?:.*?/)?release-v?(\d[\d-]*)\.tar\.gz
+Version: 5
 
-# http://search.cpan.org/dist/BioPerl-Run/   .*/BioPerl-Run-v?(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz|zip)$
+Template: Github
+Project: bioperl-run
+Owner: bioperl
+# Workaround upstream's 07-branch; use dots for upstream dashes.
+UVersion-Mangle: s/^0/0./; s/-/./g



View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7a192d251c38e1fceea12f95e38a51e60ee68e71...b5ffc81ad193a19dfb7ab7493d596ca54947661f

-- 
View it on GitLab: https://salsa.debian.org/med-team/bioperl-run/-/compare/7a192d251c38e1fceea12f95e38a51e60ee68e71...b5ffc81ad193a19dfb7ab7493d596ca54947661f
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