installing macqiime

Within the span of 1 week, I set up my new super-powerful Mac Pro, we got all of the ZEN sequence data back, and QIIME version 1.9 is live! I also posted my IPython notebook for a basic QIIME analysis.http://jennomics.github.io/QIIMEbyJennomics/

Quite a confluence of events…

Anyway… I’m christening my new machine with QIIME.

Notes on macqiime install:

1. I went through the installation instructions, including the optional add-ons with no glitches here:

http://www.wernerlab.org/software/macqiime/macqiime-installation#install

2. I ignored AmpliconNoise because I do not use 454 data.

3. I could not get Topiary Explorer to work. At first, there was a problem with the security, but I figured out how to add exceptions, but then it still didn’t work, and the error message said: “Unable to launch application.” Then, I clicked on the Details button, and I think this describes the problem:

Caused by: java.net.URISyntaxException: Relative path in absolute URI: file://topiaryexplorer1.0.jar

But, I’m not sure how to fix it, so I decided to move on and come back to Topiary Explorer when/if I need it.

4. In the bit about installing R, I noticed this:

Please note that even if you installed R and these libraries previously for MacQIIME 1.8.0, you should still upgrade to/install the latest version of R, 3.1.2, and re-install all these R packages to get everything working.

And, that’s how I learned that QIIME 1.9 was out there. BUT, it doesn’t look like macqiime has been updated, so it installed QIIME 1.8 instead. Maybe that’s because it’s a “release candidate” at this point? Anyway, I’ll have to go back and update QIIME somehow. Macqiime appears to be working. See below for the output of print_qiime_config.py -t

System information
==================
Platform:   darwin
Python version:   2.7.3 (default, Dec 19 2012, 09:12:08) [GCC 4.2.1 (Apple Inc. build 5666) (dot 3)]
Python executable:   /macqiime/bin/python

Dependency versions
===================
PyCogent version:   1.5.3
NumPy version:   1.7.1
matplotlib version:   1.1.0
biom-format version:   1.3.1
qcli version:   0.1.0
QIIME library version:   1.8.0
QIIME script version:   1.8.0
PyNAST version (if installed):   1.2.2
Emperor version:   0.9.3
RDP Classifier version (if installed):   rdp_classifier-2.2.jar
Java version (if installed):   Not installed.

QIIME config values
===================
blastmat_dir:   None
sc_queue:   all.q
topiaryexplorer_project_dir:   None
pynast_template_alignment_fp:   /macqiime/greengenes/core_set_aligned.fasta.imputed
cluster_jobs_fp:   /macqiime/QIIME/bin/start_parallel_jobs.py
pynast_template_alignment_blastdb:   None
assign_taxonomy_reference_seqs_fp:   /macqiime/greengenes/gg_13_8_otus/rep_set/97_otus.fasta
torque_queue:   friendlyq
template_alignment_lanemask_fp:   /macqiime/greengenes/lanemask_in_1s_and_0s
jobs_to_start:   1
cloud_environment:   False
qiime_scripts_dir:   /macqiime/QIIME/bin/
denoiser_min_per_core:   50
working_dir:   /tmp/
python_exe_fp:   /macqiime/bin/python
temp_dir:   /tmp/
blastall_fp:   blastall
seconds_to_sleep:   60
assign_taxonomy_id_to_taxonomy_fp:   /macqiime/greengenes/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt
….F…………………………
======================================================================
FAIL: test_ampliconnoise_install (__main__.QIIMEDependencyFull)
AmpliconNoise install looks sane.
———————————————————————-
Traceback (most recent call last):
File “/macqiime/QIIME/bin/print_qiime_config.py”, line 392, in test_ampliconnoise_install
“$PYRO_LOOKUP_FILE variable is not set. See %s for help.” % url)
AssertionError: $PYRO_LOOKUP_FILE variable is not set. See http://qiime.org/install/install.html#ampliconnoise-install-notes for help.