====== QIIME ======
QIIME™ (canonically pronounced chime) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.

===== Information =====

  * Version: 1.9.1
  * Added: March, 2017
  * Link: http://qiime.org/

===== Usage =====

See versions of qiime which are available:
<code>$ module avail qiime</code>

Load a particular version:

<code>$ module load qiime/1.9.1</code>

===== Installation ======
Notes from the sysadmin during installation:

<code>$ cd /tmp
$ wget https://www.python.org/ftp/python/2.7.13/Python-2.7.13.tar.xz
$ tar xf Python-2.7.13.tar.xz
$ cd Python-2.7.13
$ scl enable devtoolset-2 bash
$ ./configure --prefix=/export/apps/qiime/1.9.1 --enable-optimizations
$ make -j4
$ sudo mkdir -p /export/apps/qiime/1.9.1
$ sudo chown -R aorth:aorth /export/apps/qiime/1.9.1
$ make install
$ make maninstall
$ exit (from devtoolset)
$ wget https://bootstrap.pypa.io/get-pip.py -O /tmp/get-pip.py
$ /export/apps/qiime/1.9.1/bin/python /tmp/get-pip.py
$ /export/apps/qiime/1.9.1/bin/pip install numpy
$ /export/apps/qiime/1.9.1/bin/pip install qiime
# Fix problem with tkinter by changing the backend from TkAgg to Agg in: /export/apps/qiime/1.9.1/lib/python2.7/site-packages/matplotlib/mpl-data/matplotlibrc
$ cp /export/apps/qiime/1.9.1/lib/python2.7/site-packages/qiime/support_files/qiime_config /export/apps/qiime/1.9.1/qiime_config
$ print_qiime_config.py -t
$ sudo chown -R root:root /export/apps/qiime/1.9.1</code>

A dedicated Python installation is recommended so that QIIME can have complete control over the packages it needs to install without conflicting with the system's Python.