[Debian-med-packaging] Packaging Spades (Was: [spades] branch master created (now a2fa706))

[Sascha Steinbiss]

Hi Afif,

many thanks from me as well...!
I had also looked at spades and updated to he current version but didn't
commit anything because I ran into the problems mentioned by Andreas as
well (unable to find 'simplification.info').
Unfortunately spades is a dependency for some of our Sanger tools, e.g.
circlator or ariba.

Cheers
Sascha

On 23/11/2015 12:02, Andreas Tille wrote:
> Hi Afif,
> 
> it is **really** welcome that you intend to care for spades.  I will
> remove my SVN commits to make sure nobody will be confused.  Please note
> that I had trouble with running the test suite and thus failed to do a
> final upload.  The problems occured when I tried
> 
>     spades -1 ecoli_1K_1.fq.gz -2 ecoli_1K_2.fq.gz -o tmp
> 
> I also had *severe* problems to replace some Debian packaged tools (I
> guess the deactivated patches might not apply to the latest upstream but
> should be easy to adapt).  It turned out that Spades broke in a *very*
> strange way and I was not yet able to track this down.
> 
> Feel free to discuss any issues here on the list.
> 
> I kind regards
> 
>        Andreas.
> 
> 
> On Mon, Nov 23, 2015 at 11:19:01AM +0000, Afif Elghraoui wrote:
>> This is an automated email from the git hooks/post-receive script.
>>
>> afif-guest pushed a change to branch master
>> in repository spades.
>>
>>         at  a2fa706   Set Vcs fields to point to git
>>
>> This branch includes the following new commits:
>>
>>        new  9728866   Inject initial (not yet working) packaging for spades
>>        new  5b01563   Thanks to gregor hermann for the hint to the watch file
>>        new  cf53945   Files layout is a bit hackish but works for the first tests
>>        new  99af06b   Do not install license copies
>>        new  3ad0116   Add help2man based manpages
>>        new  67047f2   Do not install code copies of python-yaml and python-joblib and rather use Debian packaged code
>>        new  65daf15   Deal with some code copies, document others (more to come)
>>        new  5f3cb0f   Add upstream contact
>>        new  524a185   Move debian/upstream to debian/upstream/metadata
>>        new  531a62a   Some steps forward to adapt to latest version 3.5.  There is a lot work remaining.  For the moment it does not even build in pbuilder since it depends on a cmake control file in a not yet released bamtools package (I'll see whether this can be avoided)
>>        new  0a8d3d7   Enable pbuilder builds
>>        new  37438f9   Better organising of patches
>>        new  c5337b5   Fix spacing in patches
>>        new  ac1cfa1   Try to create patches acceptable by upstream
>>        new  b3256d5   Get something that somehow builds and passes the test.  Keep on with the replacement of code copies
>>        new  c59fd4c   Use debian's own boots library
>>        new  519b959   Strange error in test suite is caused by using Debian packaged bamtools - at least when linked this way.
>>        new  70ab84e   led to exclude yaml-cpp :-(
>>        new  b15cbaf   initial upstream branch
>>        new  7dd7202   Merge branch 'upstream'
>>        new  14f4c34   Imported Upstream version 3.6.2+dfsg
>>        new  a3c9270   Imported Upstream version 3.6.2+dfsg
>>        new  9435974   Merge tag 'upstream/3.6.2+dfsg'
>>        new  e619f1a   Update changelog for new release
>>        new  16ed1d0   Refresh patches
>>        new  81d17e9   Join the uploaders list
>>        new  a2fa706   Set Vcs fields to point to git
>>
>> The 27 revisions listed above as "new" are entirely new to this
>> repository and will be described in separate emails.  The revisions
>> listed as "adds" were already present in the repository and have only
>> been added to this reference.
>>
>>
>> -- 
>> Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git
>>
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> 


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