Dear Nadiya, thanks for commiting your packaging attempt for gatb-core which is a requirement to update minia to its latest version. Here are some comments:
1. Somehow the repository is lacking the upstream and pristine-tar branch. While you could probably do git branch upstream gbp import-orig --pristine-tar /path/to/gatb-core_1.3.0.orig.tar.gz to fix this you might possibly start from scratch as described in Debian Med policy[1] in paragraph To create a new local git repository Both should give you somehow the same result but may be the latter is better for educational reasons since this should be the more straightforward way to create a repository. If you start from scratch you need to ssh git.debian.org "rm -rf /git/debian-med/gatb-core.git" first and recreate the repository. Hint for creating new repositories on git.debian.org: I have written a script which injects an existing local repository on alioth but it relies on correct Vcs-Git field (so read below first) 2. debian/changelog * Please use target distribution UNRELEASED (instead of unstable) as long as the package is not uploaded. This is the flag for other developers that this is work in progress. * Use your developer ID (identically as it is in debian/control field Uploaders as changelog owner instead of DMTP 3. debian/control * I'm usuall doing cme fix dpkg-control to fix issues in this file. It is advisable to use cme from unstable (and the cme modules mentioned in the policy) If you apply thisit leads to the following diff diff --git a/debian/control b/debian/control index 8e3ab4e..8fc0440 100644 --- a/debian/control +++ b/debian/control @@ -1,17 +1,18 @@ Source: gatb-core -Section: science -Priority: optional Maintainer: Debian Med Packaging Team <debian-med-packag...@lists.alioth.debian.org> Uploaders: Nadiya Sitdykova <rovensk...@gmail.com> +Section: science +Priority: optional Build-Depends: debhelper (>= 10) -Standards-Version: 3.9.8 -Homepage: https://github.com/GATB/gatb-core -Vcs-Git: git://anonscm.debian.org/debian-med/gatb-core.git +Standards-Version: 4.1.1 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/gatb-core.git +Vcs-Git: https://anonscm.debian.org/git/debian-med/gatb-core.git +Homepage: https://github.com/GATB/gatb-core Package: gatb-core Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} +Depends: ${shlibs:Depends}, + ${misc:Depends} Description: The Genome Analysis Toolbox with de-Bruijn graph The GATB-CORE project provides a set of highly efficient algorithms to analyse NGS data sets. These methods enable * The cruxial diff item is +Vcs-Git: https://anonscm.debian.org/git/debian-med/gatb-core.git ^^^^^ ^^^ If you either use cme (as I would recommend) or at least fix this one you can use my script to inject local repositories into git.debian.org This can be used by svn checkout svn://anonscm.debian.org/debian-med/trunk/helper-scripts /tmp /tmp/helper-scripts/inject-into-alioth-git which is using the Vcs-Git field. (But keep on reading before you do this ...) 4. debian/copyright * I was using licensecheck -r * and realised that in gatb-core/thirdparty are several code copies of third party software like boost, hdf5 and json. Now comes the tricky part of packing since this code should be removed (well, actually you only need to make sure it is not used at build time but the most save way to make this sure is to remove it and if you would leave it you need to document all the licenses in d/copyright which is pretty boring for not used code chunks). The removal of code can be easily done as described in the wiki[2]. If you follow this I'd recommend the following changes: diff --git a/debian/changelog b/debian/changelog index 0518e36..8550ec5 100644 --- a/debian/changelog +++ b/debian/changelog @@ -1,4 +1,4 @@ -gatb-core (1.3.0-1) unstable; urgency=medium +gatb-core (1.3.0+dfsg-1) unstable; urgency=medium * Initial release (Closes: #873044) diff --git a/debian/copyright b/debian/copyright index 508ae6b..2e264fd 100644 --- a/debian/copyright +++ b/debian/copyright @@ -1,6 +1,9 @@ Format: https://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: gatb-core Source: https://github.com/GATB/gatb-core +Files-Excluded: gatb-core/thirdparty/boost + gatb-core/thirdparty/hdf5 + gatb-core/thirdparty/json Files: * Copyright: © 2014-2017 Genscale research team diff --git a/debian/watch b/debian/watch index 970f806..b6ae08b 100644 --- a/debian/watch +++ b/debian/watch @@ -1,6 +1,7 @@ version=4 # New files on Github +opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \ https://github.com/GATB/gatb-core/releases .*/archive/v(\d[\d.-]+)\.(?:tar(?:\.gz|\.bz2)?|tgz) Then you simply do uscan --verbose --force-download and uscan will provide you with a stripped down tarball without the code mentioned in Files-Excluded. Now you need to create a quilt patch to exclude these subdirs from gatb-core/thirdparty/CMakeLists.txt and convince cmake to find the according Debian packaged versions of the code. I have not checked this but you are kindly invited to ask here or at debian-ment...@lists.debian.org for help and advise. Since I know you from DebConf I like to add that there is really no shame in this and the fact that I'm ranking on place 7 on the Debian Mentors stats[3] is mostly since I'm *asking* there a lot and way less since I'm answering questions. So there is really no shame in asking since you can not know everything but there are lots of helpful people around. So far my comments for the moment. Nice you have added citations in debian/upstream/metadata (there is some editor swap file left which should be removed). Thanks a lot in any case for starting to package and feel free to keep on asking here Andreas. [1] https://debian-med.alioth.debian.org/docs/policy.html#git-tips [2] https://wiki.debian.org/UscanEnhancements [3] http://blends.debian.net/liststats/authorstat_debian-mentors.png -- http://fam-tille.de