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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

Usage

See versions of qiime which are available:

$ module avail qiime

Load a particular version:

$ module load qiime/1.9.1

Installation

Notes from the sysadmin during installation:

$ 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

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.

qiime-software.txt · Last modified: 2017/03/26 19:06 by aorth