[med-svn] [Git][med-team/unicycler][master] 5 commits: Take over patch from 0.5.1+dfsg-2 ro build with SeqAn 2.5.0 Closes: #1126255
Andreas Tille (@tille)
gitlab at salsa.debian.org
Tue May 5 10:15:30 BST 2026
Andreas Tille pushed to branch master at Debian Med / unicycler
Commits:
2b0eb0f4 by Andreas Tille at 2026-05-05T10:04:49+02:00
Take over patch from 0.5.1+dfsg-2 ro build with SeqAn 2.5.0 Closes: #1126255
- - - - -
cf5f80f1 by Andreas Tille at 2026-05-05T11:03:11+02:00
debian/tests/control: Drop restriction skip-not-installable and use Architecture: amd64 instead
- - - - -
914175c8 by Andreas Tille at 2026-05-05T11:03:56+02:00
d/watch: version=5
- - - - -
a59b98d6 by Andreas Tille at 2026-05-05T11:08:46+02:00
cme fix dpkg-control
- - - - -
8ac2edbe by Andreas Tille at 2026-05-05T11:13:19+02:00
Upload to unstable
- - - - -
6 changed files:
- debian/changelog
- debian/control
- + debian/patches/0004-Upgrade-to-SeqAn-2.5.0.patch
- debian/patches/series
- debian/tests/control
- debian/watch
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+unicycler (0.5.1+dfsg-4) unstable; urgency=medium
+
+ * Take over patch from 0.5.1+dfsg-2 ro build with SeqAn 2.5.0
+ Closes: #1126255
+ * debian/tests/control: Drop restriction skip-not-installable and use
+ Architecture: amd64 instead
+ * d/watch: version=5
+ * cme fix dpkg-control
+
+ -- Andreas Tille <tille at debian.org> Tue, 05 May 2026 11:09:34 +0200
+
unicycler (0.5.1+dfsg-3) unstable; urgency=medium
* Team upload.
@@ -8,6 +19,15 @@ unicycler (0.5.1+dfsg-3) unstable; urgency=medium
-- Alexandre Detiste <tchet at debian.org> Wed, 05 Feb 2025 21:27:11 +0100
+unicycler (0.5.1+dfsg-2) experimental; urgency=medium
+
+ * Team upload.
+ * d/control: Experimental rebuild using the 3rd release candidate of
+ SeqAn 2.5.0
+ * Added patch for the explicit seqan2 namespace.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 25 Nov 2024 14:27:41 +0100
+
unicycler (0.5.1+dfsg-1.1) unstable; urgency=medium
* Team upload.
=====================================
debian/control
=====================================
@@ -1,25 +1,26 @@
Source: unicycler
+Standards-Version: 4.7.4
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Andreas Tille <tille at debian.org>,
- Liubov Chuprikova <chuprikovalv at gmail.com>
+Uploaders:
+ Andreas Tille <tille at debian.org>,
+ Liubov Chuprikova <chuprikovalv at gmail.com>,
Section: science
-Priority: optional
-Build-Depends: debhelper-compat (= 13),
- dh-sequence-python3,
- python3-all,
- python3-setuptools,
- default-jdk <!nocheck>,
- bcftools,
- bowtie2 <!nocheck>,
- miniasm,
- ncbi-blast+ <!nocheck>,
- pilon <!nocheck>,
- racon,
- samtools <!nocheck>,
- spades (>= 3.14),
- libseqan2-dev,
- zlib1g-dev
-Standards-Version: 4.7.0
+Build-Depends:
+ debhelper-compat (= 13),
+ dh-sequence-python3,
+ python3-all,
+ python3-setuptools,
+ default-jdk <!nocheck>,
+ bcftools,
+ bowtie2 <!nocheck>,
+ miniasm,
+ ncbi-blast+ <!nocheck>,
+ pilon <!nocheck>,
+ racon,
+ samtools <!nocheck>,
+ spades,
+ libseqan2-dev,
+ zlib1g-dev,
Vcs-Browser: https://salsa.debian.org/med-team/unicycler
Vcs-Git: https://salsa.debian.org/med-team/unicycler.git
Homepage: https://github.com/rrwick/Unicycler
@@ -27,19 +28,21 @@ Rules-Requires-Root: no
Package: unicycler
Architecture: any
-Depends: ${python3:Depends},
- ${shlibs:Depends},
- ${misc:Depends},
- default-jre,
- bcftools,
- bowtie2,
- miniasm,
- ncbi-blast+,
- pilon,
- racon,
- samtools,
- spades (>= 3.14)
-Recommends: unicycler-data
+Depends:
+ ${python3:Depends},
+ ${shlibs:Depends},
+ ${misc:Depends},
+ default-jre,
+ bcftools,
+ bowtie2,
+ miniasm,
+ ncbi-blast+,
+ pilon,
+ racon,
+ samtools,
+ spades,
+Recommends:
+ unicycler-data,
Description: hybrid assembly pipeline for bacterial genomes
Unicycler is an assembly pipeline for bacterial genomes. It can assemble
Illumina-only read sets where it functions as a SPAdes-optimiser. It can
@@ -50,7 +53,8 @@ Description: hybrid assembly pipeline for bacterial genomes
Package: unicycler-data
Architecture: all
Multi-Arch: foreign
-Depends: ${misc:Depends}
+Depends:
+ ${misc:Depends},
Description: hybrid assembly pipeline for bacterial genomes (data package)
Unicycler is an assembly pipeline for bacterial genomes. It can assemble
Illumina-only read sets where it functions as a SPAdes-optimiser. It can
=====================================
debian/patches/0004-Upgrade-to-SeqAn-2.5.0.patch
=====================================
@@ -0,0 +1,161 @@
+From: "Michael R. Crusoe" <crusoe at debian.org>
+Date: Mon, 25 Nov 2024 14:22:44 +0100
+Subject: Upgrade to SeqAn 2.5.0
+
+---
+ Makefile | 2 +-
+ unicycler/include/consensus_align.h | 2 +-
+ unicycler/include/global_align.h | 2 +-
+ unicycler/include/overlap_align.h | 2 +-
+ unicycler/include/path_align.h | 2 +-
+ unicycler/include/random_alignments.h | 2 +-
+ unicycler/include/scoredalignment.h | 2 +-
+ unicycler/include/semi_global_align.h | 2 +-
+ unicycler/include/semi_global_align_exhaustive.h | 2 +-
+ unicycler/include/start_end_align.h | 2 +-
+ unicycler/src/consensus_align.cpp | 2 +-
+ 11 files changed, 11 insertions(+), 11 deletions(-)
+
+diff --git a/Makefile b/Makefile
+index 1e294f3..3f111de 100644
+--- a/Makefile
++++ b/Makefile
+@@ -67,7 +67,7 @@ CXXFLAGS ?= -Wall -Wextra -pedantic -mtune=native
+
+
+ # These flags are required for the build to work.
+-FLAGS = -std=c++14 -Iunicycler/include -fPIC
++FLAGS = -std=c++17 -Iunicycler/include -fPIC
+ LDFLAGS += -shared -lz
+
+
+diff --git a/unicycler/include/consensus_align.h b/unicycler/include/consensus_align.h
+index 224487b..423fa32 100644
+--- a/unicycler/include/consensus_align.h
++++ b/unicycler/include/consensus_align.h
+@@ -16,7 +16,7 @@
+ #include <seqan/score.h>
+ #include <seqan/consensus.h>
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Functions that are called by the Python script must have C linkage, not C++ linkage.
+ extern "C" {
+diff --git a/unicycler/include/global_align.h b/unicycler/include/global_align.h
+index 580efe6..90a071a 100644
+--- a/unicycler/include/global_align.h
++++ b/unicycler/include/global_align.h
+@@ -17,7 +17,7 @@
+ #include "scoredalignment.h"
+
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Functions that are called by the Python script must have C linkage, not C++ linkage.
+ extern "C" {
+diff --git a/unicycler/include/overlap_align.h b/unicycler/include/overlap_align.h
+index 15b151b..00b7b70 100644
+--- a/unicycler/include/overlap_align.h
++++ b/unicycler/include/overlap_align.h
+@@ -15,7 +15,7 @@
+
+ #include <seqan/sequence.h>
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Functions that are called by the Python script must have C linkage, not C++ linkage.
+ extern "C" {
+diff --git a/unicycler/include/path_align.h b/unicycler/include/path_align.h
+index 06392dc..641f58e 100644
+--- a/unicycler/include/path_align.h
++++ b/unicycler/include/path_align.h
+@@ -17,7 +17,7 @@
+ #include "scoredalignment.h"
+
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Functions that are called by the Python script must have C linkage, not C++ linkage.
+ extern "C" {
+diff --git a/unicycler/include/random_alignments.h b/unicycler/include/random_alignments.h
+index 1fea9f6..29f5081 100644
+--- a/unicycler/include/random_alignments.h
++++ b/unicycler/include/random_alignments.h
+@@ -18,7 +18,7 @@
+ #include "scoredalignment.h"
+ #include <mutex>
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Functions that are called by the Python script must have C linkage, not C++ linkage.
+ extern "C" {
+diff --git a/unicycler/include/scoredalignment.h b/unicycler/include/scoredalignment.h
+index f6bd13b..a1ef902 100644
+--- a/unicycler/include/scoredalignment.h
++++ b/unicycler/include/scoredalignment.h
+@@ -17,7 +17,7 @@
+ #include <seqan/basic.h>
+ #include <seqan/align.h>
+
+-using namespace seqan;
++using namespace seqan2;
+
+ enum CigarType {MATCH, INSERTION, DELETION, CLIP, NOTHING};
+
+diff --git a/unicycler/include/semi_global_align.h b/unicycler/include/semi_global_align.h
+index 4f558ab..35b5d63 100644
+--- a/unicycler/include/semi_global_align.h
++++ b/unicycler/include/semi_global_align.h
+@@ -26,7 +26,7 @@
+ #include "ref_seqs.h"
+ #include "nanoflann.hpp"
+
+-using namespace seqan;
++using namespace seqan2;
+ using namespace nanoflann;
+
+ typedef std::pair<int, int> StartEndRange;
+diff --git a/unicycler/include/semi_global_align_exhaustive.h b/unicycler/include/semi_global_align_exhaustive.h
+index 38f96e5..abde7d6 100644
+--- a/unicycler/include/semi_global_align_exhaustive.h
++++ b/unicycler/include/semi_global_align_exhaustive.h
+@@ -17,7 +17,7 @@
+ #include "scoredalignment.h"
+
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Functions that are called by the Python script must have C linkage, not C++ linkage.
+ extern "C" {
+diff --git a/unicycler/include/start_end_align.h b/unicycler/include/start_end_align.h
+index 9668abe..28cbd30 100644
+--- a/unicycler/include/start_end_align.h
++++ b/unicycler/include/start_end_align.h
+@@ -15,7 +15,7 @@
+
+ #include <seqan/sequence.h>
+
+-using namespace seqan;
++using namespace seqan2;
+
+ // Functions that are called by the Python script must have C linkage, not C++ linkage.
+ extern "C" {
+diff --git a/unicycler/src/consensus_align.cpp b/unicycler/src/consensus_align.cpp
+index 2194061..7197d3e 100644
+--- a/unicycler/src/consensus_align.cpp
++++ b/unicycler/src/consensus_align.cpp
+@@ -21,7 +21,7 @@
+ #include "semi_global_align.h"
+ #include "string_functions.h"
+
+-using namespace seqan;
++using namespace seqan2;
+
+ char * multipleSequenceAlignment(char * sequences[], char * qualities[], unsigned long count,
+ unsigned int bandwidth, int matchScore, int mismatchScore,
=====================================
debian/patches/series
=====================================
@@ -2,4 +2,5 @@ spades.patch
# bowtie.patch
install_wo_extra_steps.patch
append_flags
+0004-Upgrade-to-SeqAn-2.5.0.patch
leftover-syntax-warnings.patch
=====================================
debian/tests/control
=====================================
@@ -1,4 +1,5 @@
Tests: run-unit-test
Depends:
@,
-Restrictions: allow-stderr, skip-not-installable
+Restrictions: allow-stderr
+Architecture: amd64
=====================================
debian/watch
=====================================
@@ -1,4 +1,7 @@
-version=4
+Version: 5
-opts="repacksuffix=+dfsg,dversionmangle=auto,filenamemangle=s%(?:.*?)?v?(\d[\d.]*)\.tar\.gz%@PACKAGE at -$1.tar.gz%" \
- https://github.com/rrwick/Unicycler/tags .*/v?@ANY_VERSION@@ARCHIVE_EXT@
+Template: Github
+Owner: rrwick
+Project: Unicycler
+Dversion-Mangle: auto
+Repack-Suffix: +dfsg
View it on GitLab: https://salsa.debian.org/med-team/unicycler/-/compare/90f19fa7d13763bcd65d68cd7fdcff8a6af06cc3...8ac2edbe6ec058bdf23ce3549fa1f3450eb5143e
--
View it on GitLab: https://salsa.debian.org/med-team/unicycler/-/compare/90f19fa7d13763bcd65d68cd7fdcff8a6af06cc3...8ac2edbe6ec058bdf23ce3549fa1f3450eb5143e
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