[Debian-med-packaging] Bug#682199: Packaging biom-format for Debian (Was: Bug#682199: qiime: Needs function from biom-format.org, which is not packaged.)

[Greg Caporaso]

Hi Andreas,
Thanks for getting in touch about this. The biom-format project is
under GPL. I'll also make sure that we drop the OS X files next time
we do a release build.

Greg

On Fri, Jul 20, 2012 at 3:29 AM, Andreas Tille <tille at debian.org> wrote:
> Hi Greg,
>
> I try to fix a bug report against the Debian packaged Qiime.  You might
> possibly know that the Debian Med project tries to inject any program
> with relevance for medical care and microbiological research straight
> into Debian for the comfort of users working in this field.
>
> When I started packaging[1] I realised that I can not find any licensing
> information neither at biom-format.org website nor in the downloadable
> tarball.  Could you please clarify the licensing conditions to enable us
> distributing this software in Debian?
>
> I also have a remark about your upstream tarball: It contains a lot of
> "._*" files which are somehow remainings from Mac OSX.  It would be nice
> if these files could be stripped from the tarball.
>
> Kind regards
>
>        Andreas.
>
> [1]  http://svn.debian.org/wsvn/debian-med/trunk/packages/python-biom-format/trunk/
>
> On Fri, Jul 20, 2012 at 05:55:49PM +0900, Charles Plessy wrote:
>> Package: qiime
>> Version: 1.5.0-1
>> Severity: normal
>>
>> Hi all,
>>
>> /usr/lib/qiime/bin/subsample_fasta.py seems to need functions from a "biom" module,
>> that apparently is not packaged (http://biom-format.org/).
>>
>> $ /usr/lib/qiime/bin/subsample_fasta.py
>> Traceback (most recent call last):
>>   File "/usr/lib/qiime/bin/subsample_fasta.py", line 15, in <module>
>>     from qiime.util import parse_command_line_parameters, get_options_lookup,\
>>   File "/usr/lib/python2.7/dist-packages/qiime/util.py", line 41, in <module>
>>     from biom.table import DenseTable
>> ImportError: No module named biom.table
>>
>> Cheers,
>>
>
> --
> http://fam-tille.de