[Bio-Linux] Qiime Support packages missing?

[Tim Booth]

Hi James,

There are a few dependencies missing on Bio-Linux QIIME compared to the
Virtual Box version, and a few of the tool dependencies are not the
stipulated versions that QIIME says to use.  You are right that
qiime-deploy is a cumbersome solution and that's why QIIME on Bio-Linux
is installed via versions of the Debian Med packages - see
https://packages.debian.org/source/sid/qiime

This enables everyone to get updates to QIIME from the system Update
Manager, but it does also mean the QIIME system is not identical to the
one you get by running qiime-deploy, and also that new dependencies have
to be manually added as packages.

In the case of ea-utils, I'd not prioritised adding it as
"print_qiime_config -t" doesn't ask for it and no other QIIME users have
asked me for it either, but you are right it does look like something we
need.  I'll add it to the package repo now.

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