[med-svn] [Git][med-team/bandage][master] 12 commits: routine-update: Standards-Version: 4.5.0
Andreas Tille
gitlab at salsa.debian.org
Fri May 29 20:36:59 BST 2020
Andreas Tille pushed to branch master at Debian Med / bandage
Commits:
35ececb5 by Andreas Tille at 2020-05-29T17:51:57+02:00
routine-update: Standards-Version: 4.5.0
- - - - -
a4a3a2a8 by Andreas Tille at 2020-05-29T17:51:58+02:00
routine-update: debhelper-compat 13
- - - - -
55fa99aa by Andreas Tille at 2020-05-29T17:52:03+02:00
routine-update: Remove trailing whitespace in debian/control
- - - - -
6bdda514 by Andreas Tille at 2020-05-29T17:52:03+02:00
routine-update: Add salsa-ci file
- - - - -
7228905e by Andreas Tille at 2020-05-29T17:52:03+02:00
routine-update: Rules-Requires-Root: no
- - - - -
2da90853 by Andreas Tille at 2020-05-29T17:52:05+02:00
Set upstream metadata fields: Bug-Database, Bug-Submit.
Fixes: lintian: upstream-metadata-missing-bug-tracking
See-also: https://lintian.debian.org/tags/upstream-metadata-missing-bug-tracking.html
- - - - -
cacd2864 by Andreas Tille at 2020-05-29T17:52:05+02:00
Remove obsolete field Name from debian/upstream/metadata (already present in machine-readable debian/copyright).
- - - - -
88094ff7 by Andreas Tille at 2020-05-29T17:55:02+02:00
New upstream version 0.8.1
- - - - -
a749c947 by Andreas Tille at 2020-05-29T17:55:38+02:00
Update upstream source from tag 'upstream/0.8.1'
Update to upstream version '0.8.1'
with Debian dir 82314ee6fcf9c02738b403837fd2e24d01bbd136
- - - - -
af14c4ff by Andreas Tille at 2020-05-29T19:53:27+02:00
Fix permissions of examples
- - - - -
b96d4bc9 by Andreas Tille at 2020-05-29T21:20:45+02:00
Provide example data in different binary package
- - - - -
ef059f6b by Andreas Tille at 2020-05-29T21:36:44+02:00
Upload to unstable
- - - - -
11 changed files:
- − .gitignore
- debian/README.test
- + debian/bandage-examples.install
- + debian/bandage.install
- debian/changelog
- − debian/compat
- debian/control
- − debian/examples
- debian/rules
- + debian/salsa-ci.yml
- debian/upstream/metadata
Changes:
=====================================
.gitignore deleted
=====================================
@@ -1,13 +0,0 @@
-# emacs specific files
-.tasks.org
-.org-id-locations
-\#*
-*~
-.#*
-\#*\#
-*.log
-.DS_Store
-
-# folder
-venv/
-.pc/
=====================================
debian/README.test
=====================================
@@ -5,4 +5,5 @@ This package can be tested by running the provided test:
sh run-unit-test
-in order to confirm its integrity.
+in order to confirm its integrity. Make sure you install
+the package bandage-examples which provides the needed data.
=====================================
debian/bandage-examples.install
=====================================
@@ -0,0 +1 @@
+tests/* usr/share/doc/bandage/examples
=====================================
debian/bandage.install
=====================================
@@ -0,0 +1 @@
+usr/bin
=====================================
debian/changelog
=====================================
@@ -1,4 +1,6 @@
-bandage (0.8.1-2) UNRELEASED; urgency=medium
+bandage (0.8.1-2) unstable; urgency=medium
+
+ * Team upload
[ Valentin Marcon ]
* Correct DOI
@@ -10,6 +12,17 @@ bandage (0.8.1-2) UNRELEASED; urgency=medium
* Add autopkgtests
* Install docs
+ [ Andreas Tille ]
+ * Standards-Version: 4.5.0 (routine-update)
+ * debhelper-compat 13 (routine-update)
+ * Remove trailing whitespace in debian/control (routine-update)
+ * Add salsa-ci file (routine-update)
+ * Rules-Requires-Root: no (routine-update)
+ * Set upstream metadata fields: Bug-Database, Bug-Submit.
+ * Remove obsolete field Name from debian/upstream/metadata (already present in
+ machine-readable debian/copyright).
+ * Fix permissions of examples
+
-- Pranav Ballaney <ballaneypranav at gmail.com> Fri, 29 May 2020 20:57:37 +0530
bandage (0.8.1-1) unstable; urgency=medium
=====================================
debian/compat deleted
=====================================
@@ -1 +0,0 @@
-11
=====================================
debian/control
=====================================
@@ -4,13 +4,14 @@ Uploaders: Cédric Lood <cedric.lood at kuleuven.be>,
Andreas Tille <tille at debian.org>
Section: science
Priority: optional
-Build-Depends: debhelper (>= 11~),
+Build-Depends: debhelper-compat (= 13),
qtbase5-dev,
libqt5svg5-dev
-Standards-Version: 4.2.1
+Standards-Version: 4.5.0
Vcs-Browser: https://salsa.debian.org/med-team/bandage
Vcs-Git: https://salsa.debian.org/med-team/bandage.git
Homepage: https://rrwick.github.io/Bandage
+Rules-Requires-Root: no
Package: bandage
Architecture: any
@@ -19,7 +20,7 @@ Depends: ${shlibs:Depends},
Description: Bioinformatics Application for Navigating De novo Assembly Graphs Easily
Bandage is a GUI program that allows users to interact with the assembly
graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and
- others.
+ others.
.
De novo assembly graphs contain not only assembled contigs but
also the connections between those contigs, which were previously not
@@ -35,5 +36,29 @@ Description: Bioinformatics Application for Navigating De novo Assembly Graphs E
More information and download links are on the Bandage website:
rrwick.github.io/Bandage
.
- The package is relevant to the field of genome assembly and will be
- maintained by the Debian Med team.
+ The package is relevant to the field of genome assembly.
+
+Package: bandage-examples
+Architecture: all
+Depends: ${misc:Depends}
+Enhances: bandage
+Description: Bioinformatics Application for Navigating De novo Assembly Graphs Easily (data)
+ Bandage is a GUI program that allows users to interact with the assembly
+ graphs made by de novo assemblers such as Velvet, SPAdes, MEGAHIT and
+ others.
+ .
+ De novo assembly graphs contain not only assembled contigs but
+ also the connections between those contigs, which were previously not
+ easily accessible. Bandage visualises assembly graphs, with connections,
+ using graph layout algorithms. Nodes in the drawn graph, which represent
+ contigs, can be automatically labelled with their ID, length or depth.
+ Users can interact with the graph by moving, labelling and colouring
+ nodes. Sequence information can also be extracted directly from the
+ graph viewer. By displaying connections between contigs, Bandage opens
+ up new possibilities for analysing and improving de novo assemblies that
+ are not possible by looking at contigs alone.
+ .
+ More information and download links are on the Bandage website:
+ rrwick.github.io/Bandage
+ .
+ The package contains some example data.
=====================================
debian/examples deleted
=====================================
@@ -1 +0,0 @@
-tests/*
\ No newline at end of file
=====================================
debian/rules
=====================================
@@ -4,13 +4,6 @@
export LC_ALL=C.UTF-8
include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
# for hardening you might like to uncomment this:
# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
@@ -27,3 +20,7 @@ override_dh_auto_configure:
dh_auto_configure
# restore original status of source dir
mv BandageTests.pro_do_not_use BandageTests.pro
+
+override_dh_fixperms:
+ dh_fixperms
+ find debian/$(DEB_SOURCE)-examples/usr/share/doc/$(DEB_SOURCE)/examples -type f -executable -exec chmod -x \{\} \;
=====================================
debian/salsa-ci.yml
=====================================
@@ -0,0 +1,4 @@
+---
+include:
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/salsa-ci.yml
+ - https://salsa.debian.org/salsa-ci-team/pipeline/raw/master/pipeline-jobs.yml
=====================================
debian/upstream/metadata
=====================================
@@ -1,4 +1,5 @@
-Name: Bandage
+Bug-Database: https://github.com/rrwick/Bandage/issues
+Bug-Submit: https://github.com/rrwick/Bandage/issues/new
Cite-As: >
Wick R.R., Schultz M.B., Zobel J. & Holt K.E. (2015).
Bandage: interactive visualisation of de novo genome assemblies.
View it on GitLab: https://salsa.debian.org/med-team/bandage/-/compare/a227d470302cd88ea167ee2abe392e6ab6278054...ef059f6bf299893471fae92bae2cb1258472b003
--
View it on GitLab: https://salsa.debian.org/med-team/bandage/-/compare/a227d470302cd88ea167ee2abe392e6ab6278054...ef059f6bf299893471fae92bae2cb1258472b003
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