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

Andreas Tille tille at debian.org
Fri Jul 20 10:29:32 UTC 2012


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



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