[Bio-Linux] Qiime Support packages missing?

[James Mategko]

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