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 <[email protected]> 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 <[email protected]>, Andreas Tille <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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