[Bio-Linux] Qiime Support packages missing?

[James Mategko]

Hi Tim,

  I installed the update in BL8 with apt-get. The qiime command I listed 
before now works perfectly.

Thank You for pushing out the update so rapidly.

- James

On 8/20/2014 4:16 AM, Tim Booth wrote:
> 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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