[Bio-Linux] Biolinux QIIME 1.9.0 release errors

[Tim Booth]

Hi Marta,

This seems to be an issue with old files being on your machine after the
update.  As you say, these seem to be a relic from QIIME 1.6, and should
not be there.

To help me diagnose the problem, could you please run the following four
commands:

dpkg -S /usr/local/bin/pick_otus.py
dpkg -S /usr/local/bin/split_libraries_fastq.py

apt-cache policy qiime
apt-cache policy bio-linux-qiime

And send me the results.

Thanks,

TIM

On Thu, 2015-04-23 at 10:00 +0100, MARTA POZUELO DEL RIO wrote:
> Good morning,
> 
> 
> After having installed the new release of qiime in my biolinux, and
> starting to use the pipeline I used for QIIME 1.8.0, I get the
> following errors in two scripts for the moment, even when calling the
> help options. 
> 
> 
> 1. For pick_otus.py script:
> 
> File "/usr/local/bin/pick_otus.py", line 18, in <module>
>     from qiime.util import get_tmp_filename
> ImportError: cannot import name get_tmp_filename
> 
> 
> 2. For split_libraries_fastq.py script: 
> 
> Traceback (most recent call last):
>   File "/usr/local/bin/split_libraries_fastq.py", line 25, in <module>
>     from qiime.quality import phred_to_ascii33, phred_to_ascii64
> 
> 
> 
> 
> For the second case, I've seen that this module disappears in QIIME
> 1.9.0, the script quality.py does not exist any more. So having a look
> at the scripts included in the packages for biolinux release, I've
> found that the version of these scripts used comes from QIIME 1.6.0. 
> 
> 
> Hope this will be solved as soon as possible!
> 
> 
> Thanks in advance.
> 
> 
> Marta
> 
> 
> 

-- 
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre 

Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB 

http://environmentalomics.org/bio-linux
+44 1491 69 2297