[med-svn] [Git][med-team/qcumber][master] 11 commits: Fix clean target. Closes: #1049117.
Santiago Vila (@sanvila)
gitlab at salsa.debian.org
Thu Nov 20 17:42:25 GMT 2025
Santiago Vila pushed to branch master at Debian Med / qcumber
Commits:
b6a28a93 by Santiago Vila at 2025-11-20T18:10:00+01:00
Fix clean target. Closes: #1049117.
- - - - -
bfadb70e by Santiago Vila at 2025-11-20T18:11:00+01:00
d/control: Drop "Rules-Requires-Root: no" (default).
- - - - -
8c86d012 by Santiago Vila at 2025-11-20T18:12:00+01:00
d/control: Drop "Priority: optional" (default).
- - - - -
755c4c90 by Santiago Vila at 2025-11-20T18:13:00+01:00
d/control: Update standards-version.
- - - - -
95bae37d by Santiago Vila at 2025-11-20T18:14:00+01:00
Patch test/.default_low_spec_test_run.yaml to use https instead of ftp.
- - - - -
670e3748 by Santiago Vila at 2025-11-20T18:15:00+01:00
d/tests: Refactor everything.
- - - - -
b9eed9ba by Camaleón at 2025-11-20T18:16:00+01:00
Add po-debconf Spanish translation. Closes: #1036374.
- - - - -
c3a11b49 by Martin Bagge at 2025-11-20T18:17:00+01:00
Add po-debconf Swedish translation. Closes: #1068856.
- - - - -
bc57ea57 by Adriano Rafael Gomes at 2025-11-20T18:18:00+01:00
Update po-debconf Brazilian Portuguese translation. Closes: #1103459.
- - - - -
d493dc4f by Santiago Vila at 2025-11-20T18:19:00+01:00
Fix wording in all debconf files.
- s/simplyfy/simplify/
- Add missing comma.
- - - - -
3a8f3720 by Santiago Vila at 2025-11-20T18:20:00+01:00
Upload for unstable as 2.3.0-3
- - - - -
18 changed files:
- debian/changelog
- + debian/clean
- debian/control
- debian/patches/series
- + debian/patches/use-https-instead-of-ftp.patch
- debian/po/ca.po
- debian/po/de.po
- + debian/po/es.po
- debian/po/fr.po
- debian/po/nl.po
- debian/po/pt.po
- debian/po/pt_BR.po
- debian/po/ru.po
- + debian/po/sv.po
- debian/po/templates.pot
- debian/templates
- debian/tests/control
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,15 +1,38 @@
-qcumber (2.3.0-3) UNRELEASED; urgency=medium
+qcumber (2.3.0-3) unstable; urgency=medium
+
+ * Team upload.
[ Andreas Tille ]
* Recommends: dwgsim, kraken
* Replace yaml.load() by yaml.safe_load()
* Fix debian/get-minikrakendb
- * bowtie2 which is not available on i386
+ * d/salsa-ci.yml: Disable build on i386.
[ Komolehin Israel Timilehin ]
- * Added Autopkgtest
+ * Added Autopkgtest.
+
+ [ Carles Pina i Estany ]
+ * Add po-debconf Catalan translation.
+
+ [ Camaleón ]
+ * Add po-debconf Spanish translation. Closes: #1036374.
+
+ [ Martin Bagge ]
+ * Add po-debconf Swedish translation. Closes: #1068856.
+
+ [ Adriano Rafael Gomes ]
+ * Update po-debconf Brazilian Portuguese translation. Closes: #1103459.
+
+ [ Santiago Vila ]
+ * Fix clean target. Closes: #1049117.
+ * d/control: Drop "Rules-Requires-Root: no" (default).
+ * d/control: Drop "Priority: optional" (default).
+ * d/control: Update standards-version.
+ * Patch test/.default_low_spec_test_run.yaml to use https instead of ftp.
+ * d/tests: Refactor everything.
+ * Fix wording in all debconf files.
- -- Komolehin Israel Timilehin <komolehinisrael at gmail.com> Fri, 08 Dec 2023 20:43:19 +0000
+ -- Santiago Vila <sanvila at debian.org> Thu, 20 Nov 2025 18:20:00 +0100
qcumber (2.3.0-2) unstable; urgency=medium
=====================================
debian/clean
=====================================
@@ -0,0 +1 @@
+config/adapters.fa
=====================================
debian/control
=====================================
@@ -2,7 +2,6 @@ Source: qcumber
Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
Uploaders: Andreas Tille <tille at debian.org>
Section: science
-Priority: optional
Build-Depends: debhelper-compat (= 13),
dh-python,
python3-all,
@@ -12,11 +11,10 @@ Build-Depends: debhelper-compat (= 13),
bowtie2,
kraken,
texlive-latex-base
-Standards-Version: 4.5.1
+Standards-Version: 4.7.2
Vcs-Browser: https://salsa.debian.org/med-team/qcumber
Vcs-Git: https://salsa.debian.org/med-team/qcumber.git
Homepage: https://gitlab.com/RKIBioinformaticsPipelines/QCumber
-Rules-Requires-Root: no
Package: qcumber
Architecture: all
=====================================
debian/patches/series
=====================================
@@ -4,3 +4,4 @@ make_executable.patch
fix_html_file_licenses.patch
add-python-shebang.patch
yaml_load.patch
+use-https-instead-of-ftp.patch
=====================================
debian/patches/use-https-instead-of-ftp.patch
=====================================
@@ -0,0 +1,23 @@
+Description: Use https instead of ftp to retrieve test data
+Author: Santiago Vila <sanvila at debian.org>
+Last-Update: 2025-11-20
+
+--- a/test/.default_low_spec_test_run.yaml
++++ b/test/.default_low_spec_test_run.yaml
+@@ -152,14 +152,14 @@
+ e_coli:
+ descriptive_name: Escherichia coli str. K-12 substr. MG1655
+ url:
+- "ftp://ftp.ncbi.nlm.nih.gov/genomes/\
++ "https://ftp.ncbi.nlm.nih.gov/genomes/\
+ all/GCF/000/005/845/GCF_000005845.2_ASM584v2/\
+ GCF_000005845.2_ASM584v2_genomic.fna.gz"
+
+ influenza_A:
+ descriptive_name: Influenza A virus (A/New York/392/2004(H3N2))
+ url:
+- "ftp://ftp.ncbi.nlm.nih.gov/genomes/\
++ "https://ftp.ncbi.nlm.nih.gov/genomes/\
+ all/GCF/000/865/085/\
+ GCF_000865085.1_ViralMultiSegProj15622/\
+ GCF_000865085.1_ViralMultiSegProj15622_genomic.fna.gz"
=====================================
debian/po/ca.po
=====================================
@@ -27,10 +27,10 @@ msgstr "Directori d'instal·lació de la base de dades del «minikraken»:"
#. Description
#: ../templates:1001
msgid ""
-"QCumber is using kraken which needs a database. To simplyfy the process of "
+"QCumber is using kraken which needs a database. To simplify the process of "
"creating the database which requires a lot of computing power there is the "
"option to download this database (see https://ccb.jhu.edu/software/"
-"kraken/). If you want to run QCumber the directory of the kraken database "
+"kraken/). If you want to run QCumber, the directory of the kraken database "
"needs to be known to the program. Please input the directory the database "
"is installed or should the database be installed by the script /usr/share/"
"doc/qcumber/get-minikrakendb."
=====================================
debian/po/de.po
=====================================
@@ -26,10 +26,10 @@ msgstr "Installationsverzeichnis der minikraken Datenbank:"
#. Description
#: ../templates:1001
msgid ""
-"QCumber is using kraken which needs a database. To simplyfy the process of "
+"QCumber is using kraken which needs a database. To simplify the process of "
"creating the database which requires a lot of computing power there is the "
"option to download this database (see https://ccb.jhu.edu/software/"
-"kraken/). If you want to run QCumber the directory of the kraken database "
+"kraken/). If you want to run QCumber, the directory of the kraken database "
"needs to be known to the program. Please input the directory the database "
"is installed or should the database be installed by the script /usr/share/"
"doc/qcumber/get-minikrakendb."
=====================================
debian/po/es.po
=====================================
@@ -0,0 +1,46 @@
+# Translation of qcumber debconf templates to Spanish.
+# Copyright (C) 2023 Camaleón <noelamac at gmail.com>
+# This file is distributed under the same license as the qcumber package.
+# Camaleón <noelamac at gmail.com>, 2023.
+#
+msgid ""
+msgstr ""
+"Project-Id-Version: qcumber\n"
+"Report-Msgid-Bugs-To: qcumber at packages.debian.org\n"
+"POT-Creation-Date: 2016-11-29 14:47+0100\n"
+"PO-Revision-Date: 2023-05-12 16:17+0200\n"
+"Language-Team: Debian Spanish <debian-l10n-spanish at lists.debian.org>\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=UTF-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+"X-Generator: Poedit 2.4.2\n"
+"Last-Translator: Camaleón <noelamac at gmail.com>\n"
+"Plural-Forms: nplurals=2; plural=(n != 1);\n"
+"Language: es\n"
+
+#. Type: string
+#. Description
+#: ../templates:1001
+msgid "Installation directory of the minikraken database:"
+msgstr "Directorio de instalación de la base de datos minikraken:"
+
+#. Type: string
+#. Description
+#: ../templates:1001
+msgid ""
+"QCumber is using kraken which needs a database. To simplify the process of "
+"creating the database which requires a lot of computing power there is the "
+"option to download this database (see https://ccb.jhu.edu/software/"
+"kraken/). If you want to run QCumber, the directory of the kraken database "
+"needs to be known to the program. Please input the directory the database "
+"is installed or should the database be installed by the script /usr/share/"
+"doc/qcumber/get-minikrakendb."
+msgstr ""
+"QCumber utiliza kraken por lo que necesita una base de datos. Para "
+"simplificar el proceso de creación de la base de datos, que requiere "
+"un uso intensivo de los recursos del sistema, puede descargar la base de "
+"datos (consulte «https://ccb.jhu.edu/software/kraken/»). Si quiere ejecutar "
+"QCumber, el programa necesita conocer la ubicación del directorio de la "
+"base de datos de kraken. Introduzca el directorio donde se encuentra "
+"instalada la base de datos o si se debe instalar la base de datos "
+"utilizando el guión «/usr/share/doc/qcumber/get-minikrakendb»."
=====================================
debian/po/fr.po
=====================================
@@ -27,10 +27,10 @@ msgstr "Répertoire d'installation de la base données minikraken :"
#. Description
#: ../templates:1001
msgid ""
-"QCumber is using kraken which needs a database. To simplyfy the process of "
+"QCumber is using kraken which needs a database. To simplify the process of "
"creating the database which requires a lot of computing power there is the "
"option to download this database (see https://ccb.jhu.edu/software/"
-"kraken/). If you want to run QCumber the directory of the kraken database "
+"kraken/). If you want to run QCumber, the directory of the kraken database "
"needs to be known to the program. Please input the directory the database "
"is installed or should the database be installed by the script /usr/share/"
"doc/qcumber/get-minikrakendb."
=====================================
debian/po/nl.po
=====================================
@@ -29,10 +29,10 @@ msgstr "Installatiemap van de minikraken-databank:"
#. Description
#: ../templates:1001
msgid ""
-"QCumber is using kraken which needs a database. To simplyfy the process of "
+"QCumber is using kraken which needs a database. To simplify the process of "
"creating the database which requires a lot of computing power there is the "
"option to download this database (see https://ccb.jhu.edu/software/"
-"kraken/). If you want to run QCumber the directory of the kraken database "
+"kraken/). If you want to run QCumber, the directory of the kraken database "
"needs to be known to the program. Please input the directory the database "
"is installed or should the database be installed by the script /usr/share/"
"doc/qcumber/get-minikrakendb."
=====================================
debian/po/pt.po
=====================================
@@ -26,10 +26,10 @@ msgstr "Directório de instalação da base de dados minikraken:"
#. Description
#: ../templates:1001
msgid ""
-"QCumber is using kraken which needs a database. To simplyfy the process of "
+"QCumber is using kraken which needs a database. To simplify the process of "
"creating the database which requires a lot of computing power there is the "
"option to download this database (see https://ccb.jhu.edu/software/"
-"kraken/). If you want to run QCumber the directory of the kraken database "
+"kraken/). If you want to run QCumber, the directory of the kraken database "
"needs to be known to the program. Please input the directory the database "
"is installed or should the database be installed by the script /usr/share/"
"doc/qcumber/get-minikrakendb."
=====================================
debian/po/pt_BR.po
=====================================
@@ -2,18 +2,17 @@
# Copyright (C) 2017 THE qcumber'S COPYRIGHT HOLDER
# This file is distributed under the same license as the qcumber package.
# José de Figueiredo <deb.gnulinux at gmail.com>, 2017.
-# Adriano Rafael Gomes <adrianorg at debian.org>, 2018.
+# Adriano Rafael Gomes <adrianorg at debian.org>, 2018-2025.
#
msgid ""
msgstr ""
"Project-Id-Version: qcumber\n"
"Report-Msgid-Bugs-To: qcumber at packages.debian.org\n"
"POT-Creation-Date: 2016-11-29 14:47+0100\n"
-"PO-Revision-Date: 2018-08-26 18:24-0300\n"
+"PO-Revision-Date: 2025-03-21 15:13-0300\n"
"Last-Translator: Adriano Rafael Gomes <adrianorg at debian.org>\n"
-"Language-Team: Brazilian Portuguese <debian-l10n-portuguese at lists.debian."
-"org>\n"
-"Language: pt_BR \n"
+"Language-Team: pt_BR <debian-l10n-portuguese at lists.debian.org>\n"
+"Language: pt_BR\n"
"MIME-Version: 1.0\n"
"Content-Type: text/plain; charset=UTF-8\n"
"Content-Transfer-Encoding: 8bit\n"
@@ -28,10 +27,10 @@ msgstr "Diretório de instalação do banco de dados minikraken:"
#. Description
#: ../templates:1001
msgid ""
-"QCumber is using kraken which needs a database. To simplyfy the process of "
+"QCumber is using kraken which needs a database. To simplify the process of "
"creating the database which requires a lot of computing power there is the "
"option to download this database (see https://ccb.jhu.edu/software/"
-"kraken/). If you want to run QCumber the directory of the kraken database "
+"kraken/). If you want to run QCumber, the directory of the kraken database "
"needs to be known to the program. Please input the directory the database "
"is installed or should the database be installed by the script /usr/share/"
"doc/qcumber/get-minikrakendb."
=====================================
debian/po/ru.po
=====================================
@@ -29,10 +29,10 @@ msgstr "Каталог установки базы данных minikraken:"
#. Description
#: ../templates:1001
msgid ""
-"QCumber is using kraken which needs a database. To simplyfy the process of "
+"QCumber is using kraken which needs a database. To simplify the process of "
"creating the database which requires a lot of computing power there is the "
"option to download this database (see https://ccb.jhu.edu/software/"
-"kraken/). If you want to run QCumber the directory of the kraken database "
+"kraken/). If you want to run QCumber, the directory of the kraken database "
"needs to be known to the program. Please input the directory the database "
"is installed or should the database be installed by the script /usr/share/"
"doc/qcumber/get-minikrakendb."
=====================================
debian/po/sv.po
=====================================
@@ -0,0 +1,36 @@
+# Translation of qcumberX debconf template to Swedish
+# Copyright (C) 2024 Martin Bagge <brother at persilja.net>
+# This file is distributed under the same license as the qcumber package.
+#
+# Martin Bagge <brother at persilja.net>, 2024
+msgid ""
+msgstr ""
+"Project-Id-Version: qcumber\n"
+"Report-Msgid-Bugs-To: qcumber at packages.debian.org\n"
+"POT-Creation-Date: 2016-11-29 14:47+0100\n"
+"PO-Revision-Date: 2024-04-12 13:25+0200\n"
+"Last-Translator: Martin Bagge <brother at persilja.net>, 2024\n"
+"Language-Team: Swedish zdebian-l10n-swedish at lists.debian.org>\n"
+"Language: sv\n"
+"MIME-Version: 1.0\n"
+"Content-Type: text/plain; charset=utf-8\n"
+"Content-Transfer-Encoding: 8bit\n"
+
+#. Type: string
+#. Description
+#: ../templates:1001
+msgid "Installation directory of the minikraken database:"
+msgstr "Sökväg för installation av minikraken-databasen?"
+
+#. Type: string
+#. Description
+#: ../templates:1001
+msgid ""
+"QCumber is using kraken which needs a database. To simplify the process of "
+"creating the database which requires a lot of computing power there is the "
+"option to download this database (see https://ccb.jhu.edu/software/"
+"kraken/). If you want to run QCumber, the directory of the kraken database "
+"needs to be known to the program. Please input the directory the database "
+"is installed or should the database be installed by the script /usr/share/"
+"doc/qcumber/get-minikrakendb."
+msgstr "QCumber använder kraken som behöver en databas. För att förenkla processen för att skapa databasen (vilket kräver ganska mycket beräkningskraft) så erbjuds alternativet att hämta databasen (läs mer på https://ccb.jhu.edu/software/kraken/). För att kunna starta QCumber, måste sökvägen till databasen vara känd av programmet. Ange var databasen finns eller kommer att finnas när scriptet /usr/share/doc/qcumber/get-minikrakendb har kört."
=====================================
debian/po/templates.pot
=====================================
@@ -27,10 +27,10 @@ msgstr ""
#. Description
#: ../templates:1001
msgid ""
-"QCumber is using kraken which needs a database. To simplyfy the process of "
+"QCumber is using kraken which needs a database. To simplify the process of "
"creating the database which requires a lot of computing power there is the "
"option to download this database (see https://ccb.jhu.edu/software/"
-"kraken/). If you want to run QCumber the directory of the kraken database "
+"kraken/). If you want to run QCumber, the directory of the kraken database "
"needs to be known to the program. Please input the directory the database "
"is installed or should the database be installed by the script /usr/share/"
"doc/qcumber/get-minikrakendb."
=====================================
debian/templates
=====================================
@@ -2,10 +2,10 @@ Template: qcumber/krakendb
Type: string
Default: /var/lib/kraken/minikraken_20141208
_Description: Installation directory of the minikraken database:
- QCumber is using kraken which needs a database. To simplyfy the process
+ QCumber is using kraken which needs a database. To simplify the process
of creating the database which requires a lot of computing power there is
the option to download this database (see
- https://ccb.jhu.edu/software/kraken/). If you want to run QCumber the
+ https://ccb.jhu.edu/software/kraken/). If you want to run QCumber, the
directory of the kraken database needs to be known to the program. Please
input the directory the database is installed or should the database be
installed by the script /usr/share/doc/qcumber/get-minikrakendb.
=====================================
debian/tests/control
=====================================
@@ -1,3 +1,3 @@
-Test-Command: sh debian/tests/run-unit-test
-Depends: dwgsim, python3-pandas, snakemake, wget
-Restrictions: allow-stderr, needs-internet
\ No newline at end of file
+Tests: run-unit-test
+Depends: dwgsim, python3-pandas, snakemake, wget, python3-biopython
+Restrictions: allow-stderr, needs-internet
=====================================
debian/tests/run-unit-test
=====================================
@@ -1,11 +1,9 @@
-#!/bin/bash
-
-
-if [ "$AUTOPKGTEST_TMP" = ""]; then
- AUTOPKGTEST_TMP=`mktemp -d /tmp/${pkg}-test.XXXX`
-
- trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
+#!/bin/sh
+set -e
+if [ "$AUTOPKGTEST_TMP" = "" ]; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXX)
+ trap "rm -rf $AUTOPKG_TMP" 0 INT QUIT ABRT PIPE TERM
fi
cd test
@@ -14,4 +12,4 @@ cd test
./test_qcumber2.py gen_test_yaml
# Run upstream test
-./test_qcumber2.py
\ No newline at end of file
+./test_qcumber2.py
View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/873a2a6288b094b481bbe48294d6ceabb18ff40f...3a8f3720ff299c4b7ff4e43b5eb2e93bd568c324
--
View it on GitLab: https://salsa.debian.org/med-team/qcumber/-/compare/873a2a6288b094b481bbe48294d6ceabb18ff40f...3a8f3720ff299c4b7ff4e43b5eb2e93bd568c324
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