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

[Charles Plessy]

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,

-- Charles


-- System Information:
Debian Release: wheezy/sid
  APT prefers stable
  APT policy: (910, 'stable'), (900, 'testing'), (800, 'unstable'), (500, 'stable-updates'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 3.2.0-2-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_GB.utf8, LC_CTYPE=en_GB.utf8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages qiime depends on:
ii  king                      2.21.120420-2  interactive system for three-dimen
ii  libc6                     2.13-21        Embedded GNU C Library: Shared lib
ii  libffi5                   3.0.9-3        Foreign Function Interface library
ii  libgmp10                  2:5.0.2+dfsg-1 Multiprecision arithmetic library
ii  pynast [python-pynast]    1.1-3          alignment of short DNA sequences
ii  python                    2.6.6-14       interactive high-level object-orie
ii  python-cogent             1.5.1-2        framework for genomic biology
ii  python2.6                 2.6.6-8+b1     An interactive high-level object-o
ii  python2.7                 2.7.3-2        Interactive high-level object-orie

Versions of packages qiime recommends:
ii  ampliconnoise        1.25-1              Programs for the removal of noise 
ii  blast2               1:2.2.21.20090809-2 Basic Local Alignment Search Tool
ii  cd-hit               4.5.7-1             suite of programs designed to quic
pn  chimeraslayer        <none>              (no description available)
pn  fasttree             <none>              (no description available)
ii  infernal             1.0.2-1             inference of RNA secondary structu
ii  muscle               1:3.8.31-1          Multiple alignment program of prot
ii  python-matplotlib    1.1.0-1             Python based plotting system in a 
ii  python-numpy         1:1.5.1-3           Numerical Python adds a fast array
pn  rdp-classifier       <none>              (no description available)

Versions of packages qiime suggests:
pn  cytoscape                   <none>       (no description available)
ii  t-coffee                    9.02.r1228-2 Multiple Sequence Alignment

-- no debconf information

-- debsums errors found:
debsums: changed file /usr/lib/qiime/bin/subsample_fasta.py (from qiime package)