Saturday, February 26, 2011

Qiime (8) In the Virtual Box


We still have more to do in the tutorial, but this post is about the virtual machine with QIIME installed. The website discussion for this is here. My thinking is that for a real 454 or Illumina data set (which I should have at some point in the future), I will want to run "in the cloud." It's all over the web:

If you need milk, would you buy a cow ?'.


To do that I will need to get comfortable with Linux and Qiime in this environment. The Qiime website has discussion about the EC2 "image" (here), but for today's example I used the Virtual Box (VB) with Qiime.

A couple of issues had to be addressed first. There is something called "Guest Additions" that needs to be installed. The way I did it was to do:


cd /media/VBOXADDITIONS_4.0.4_70112/
./autorun.sh


and then restart the Qiime VB. The second is to train my brain to use


command (Apple symbol) on OS X
control when not in the terminal on the Virtual Box
control-shift when in terminal on the Virtual Box


And finally, I found the password (qiime---had to search the QIIME Forum for that). The Linux install doesn't have curl so I used:


wget http://bmf.colorado.edu/QIIME/qiime_tutorial-v1.2.1.zip
unzip qiime_tutorial-v1.2.1.zip
rm -r qiime_tutorial-v1.2.1.zip


Then I just followed my own instructions from here and here. I got a failure with:


plot_taxa_summary.py:  command not found


which I fixed by:


svn co https://qiime.svn.sourceforge.net/svnroot/qiime/trunk Qiime
cd Qiime
python setup.py install --install-scripts=/software/qiime-1.2.0-release/bin
cd tests
./all_tests.py



Failed the following unit tests.
/home/qiime/Qiime/tests/test_pycogent_backports/test_uclust.py
/home/qiime/Qiime/tests/test_pyronoise.py

Failed the following unit tests, in part or whole due to missing external applications.
Depending on the QIIME features you plan to use, this may not be critical.
/home/qiime/Qiime/tests/test_identify_chimeric_seqs.py
/home/qiime/Qiime/tests/test_make_per_library_sff.py
/home/qiime/Qiime/tests/test_trim_sff_primers.py
/home/qiime/Qiime/tests/test_workflow.py

Failed the following script tests.
/software/qiime-1.2.0-release/bin/process_sra_submission.py


I'm not too worried about the failures. I'll look into it.
There's a screenshot at the top of the post. Looking good.

[ UPDATE: Instructions for shared folders with the host OS here. ]

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