Re: Bug#692498: ITP: bamtools -- C++ API and toolkit for manipulating BAM (genome alignment) files
On Wed, Nov 7, 2012 at 6:21 AM, Dominique Belhachemi <domibel@debian.org> wrote:
> It is also possible to remove the third party code from the source tarball
> and from debian/copyright.
I've removed it from the master branch and modified the copyright.
What is the best way to update the source tarball?
> Please take a look at the following two patches. They add out-of-source
> support to bamtools.
>
> https://github.com/domibel/bamtools/commit/5fc8c1928eaa46fb58618db8ecb93e40cfce54ba
> https://github.com/domibel/bamtools/commit/784ff9bbf67d131bce59d548aa911e7ee8698aac
> -Dominique
>
>
> On Wed, Nov 7, 2012 at 2:59 AM, Andreas Tille <andreas@an3as.eu> wrote:
>>
>> Hi Michael,
>>
>> thanks for your effort to prepare a bamtools Debian package and also
>> notifying the Debian Med project.
>>
>> On Tue, Nov 06, 2012 at 03:16:44PM -0700, Michael Crusoe wrote:
>> > And here's the package,
>> >
>> > https://github.com/mr-c/bamtools/tree/debian
>>
>> I tried to check out this URL using
>>
>> git clone https://github.com/mr-c/bamtools/tree/debian
>> Cloning into 'debian'...
>> fatal: https://github.com/mr-c/bamtools/tree/debian/info/refs not found:
>> did you run git update-server-info on the server?
>>
>>
>> In any case I would really love if you would consider maintenance of the
>> Debian packaging at git.debian.org as it is described in Debian Med team
>> policy[1] which has a lot of advantages that might not obvious at first
>> sight (I'd happily elaborate on this if you are curious what these might
>> be.) I'd volunteer to create an initial repository - write access should
>> be easy for you because I just verified that you are member of the Alioth
>> project.
>>
>> > My packaging skills are a bit rusty, so your feedback would be
>> > appreciated.
>>
>> :)
>> I checked out the Zip archive from Github and will comment on this basis
>> below.
>>
>> > On Tue, Nov 6, 2012 at 1:28 PM, Michael Crusoe
>> > <michael.crusoe@gmail.com> wrote:
>> > > Package: wnpp
>> > > Severity: wishlist
>> > > Owner: debian-med@lists.debian.org
>> > >
>> > > * Package name : bamtools
>> > > Version : 2.2
>> > > Upstream Author : Derek Barnett <derekwbarnett@gmail.com>
>> > > * URL : https://github.com/pezmaster31/bamtools
>> > > * License : Expat
>> > > Programming Lang: C++
>> > > Description : C++ API and toolkit for manipulating BAM (genome
>> > > alignment) files
>>
>> I intended to answer in response to your ITP bug that a long description
>> is missing and it is also basically missing in your debian/control file.
>> Please try to find a more verbose description for the binary packages.
>>
>> Other issues in debian/control:
>>
>> Maintainer: great, you obviosely are aware about[1] - did I mention
>> you should consider maintenance at git.debian.org ;-)
>> Vcs-{Git,Browser}: see above, several tools are relying on this
>> Description: short description of lib and devel package should be
>> different (to tell them appart) and as I said a better
>> long description is needed
>>
>> File debian/clean: Uhmm, my packaging skills also do not seem to be up
>> to date. I never used this because I was not aware about this and
>> I definitely could have used in some cases. However, I guess you are
>> specifying most probably the wrong file - I think you want to delete
>> debian/bamtools.1 there
>>
>> File debian/libbamtools2.2.0.dir: You most probably want to append an
>> 's' to the file name - or just remove it together with the other
>> *.dirs file. Both are not needed because dh_install is clever enough
>> to create the directories. The only need to create directories that
>> way is if you want to move something around before dh_install
>>
>> File libbamtools2.2.0.manpages: Are you sure that you want to install
>> debian/bamtools-2.2.0.1 as manpage? The file name does not look at
>> all like a manpage - I would simply remove this file
>>
>> Files *.postints / *.postrm: These files are looking like usual
>> templates. I have not seen any specific use. Did I missed something?
>>
>> File debian/rules:
>>
>> 1. Please drop the comment of the dh-make template. This file is
>> actually no "Sample debian/rules that uses debhelper."
>> 2. override_dh_auto_clean is fine - but why not using debian/clean
>> for this as well (just wondering)
>> 3. get-orig-source: see below
>>
>> Missing file debian/watch: It seems bamtools relies totally in Git to
>> distribute the source. I admit we are facing such situations more and
>> more however, my personal opinion is that we should try to recommend
>> upstream to do some versioned source tarball releases to enable tools
>> like uscan detecting new versions. You could write a reasonable
>> debian/watch file which would make the get-orig-source target in
>> debian/rules unneeded. You seem to be connected to upstream and I would
>> like you to propagate this idea.
>>
>> Kind regards and many thanks for your work on this
>>
>> Andreas.
>>
>>
>> [1] http://debian-med.alioth.debian.org/docs/policy.html
>>
>> --
>> http://fam-tille.de
>>
>>
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>>
>
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