[Bio-Linux] Qiime Support packages missing?

[Tim Booth]

Dear all,

I've now added ea-utils to Bio-Linux.  The next update to QIIME will
bring in the extra package, or else you can just "apt-get install
ea-utils" if you want to join your paired-end sequences right now.  This
gets the join_paired_ends feature in QIIME working.  You might also find
the tools useful in themselves - see:

https://code.google.com/p/ea-utils/

Mostly I'll pick up missing things like this by running the QIIME
self-tests, but annoyingly the "tests/test_join_paired_ends.py"
regression test says "All OK" even if fastq-join is not available on the
system.  For reasons like this, I do appreciate users letting me know
when things are amiss.

Cheers,

TIM

On Mon, 2014-08-18 at 21:39 +0100, James Mategko wrote:
> Hello Bio-Linux community,
> 
>    Our lab group has started using Qiime and found that some of the 
> dependencies present in the Qiime Virtual Box are not present in the 
> Bio-Linux install for version 7 or 8.
> 
> Specific example:
> 
> bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py 
> -f 
> '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' 
> -r 
> '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' 
> -o '/home/bl8-beta/Desktop/qiimeTests'
> [sudo] password for bl8-beta:
> Traceback (most recent call last):
>    File "/usr/lib/qiime/bin/join_paired_ends.py", line 168, in <module>
>      main()
>    File "/usr/lib/qiime/bin/join_paired_ends.py", line 144, in main
>      working_dir = output_dir)
>    File 
> "/usr/lib/python2.7/dist-packages/qiime/pycogent_backports/fastq_join.py", 
> line 179, in join_paired_end_reads_fastqjoin
>      HALT_EXEC=HALT_EXEC)
>    File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 165, 
> in __init__
>      self._error_on_missing_application(params)
>    File "/usr/lib/python2.7/dist-packages/cogent/app/util.py", line 434, 
> in _error_on_missing_application
>      % command
> cogent.app.util.ApplicationNotFoundError: Cannot find fastq-join. Is it 
> installed? Is it in your path?
> bl8-beta at bl8beta-VirtualBox[qiimeTests] sudo qiime join_paired_ends.py 
> -f 
> '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R1_001.fastq' 
> -r 
> '/home/bl8-beta/Desktop/qiimeTests/waterSample35_S10_L001_R2_001.fastq' 
> -o '/home/bl8-beta/Desktop/qiimeTests'
> 
> The "join_paired_ends.py" feature is dependent on "fastq-join". I 
> searched my BL8 install for "fastq-join" and found no hits. However, in 
> the Qiime Virtual Box the above command works perfectly and "fastq-join" 
> is located in "/home/qiime/qiime_software/ea-utils-1.1.2-537-release". I 
> searched for a few other tools in this directory and they are also not 
> present in BL8 or BL7.
> 
> It looks like BL's install of qiime was manual rather then a 
> qiime-deploy installation, and the directory ea-utils-1.1.2-537-release 
> was not installed in BL. Our current solution is to use the Qiime VM or 
> reinstall Qiime with qiime-deploy.
> 
> Is their a less cumbersome solution to get the above command working? Is 
> there a reasion why "ea-utils-1.1.2-537-release "dir is not included in 
> the current copy of BL8?
> 
> Thank You,
> - James
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-- 
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://nebc.nerc.ac.uk
+44 1491 69 2705