QIIME 1.8

General Introduction
QIIME (pronounced "chime") stands for Quantitative Insights Into Microbial Ecology. QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data). QIIME takes users from their raw sequencing output through initial analyses such as OTU picking, taxonomic assignment, and construction of phylogenetic trees from representative sequences of OTUs, and through downstream statistical analysis, visualization, and production of publication-quality graphics. QIIME has been applied to single studies based on billions of sequences from thousands of samples.

Using QIIME 1.8

 * Login to the cheaha cluster.
 * Please run the following command to configure your environment variables for QIIME usage. You can also add this command in your bash profile (for regular qiime users).


 * QIIME is ready for usage. You can check the qiime configurations using following command

Installation notes Make following changes first module load python/python-2.7 module load mpich/mpich2-gnu module load haskell/ghc unset DISPLAY Download installation script and files git clone git://github.com/qiime/qiime-deploy.git git clone git://github.com/qiime/qiime-deploy-conf.git

Edit the folling lines in qiime-deploy-conf/qiime-1.8.0/qiime.conf so that It looks like

[global] log-level: DEBUG max-deploy-threads: 1 append-environment-to-bashrc: yes append-environment-to-bashprofile: no [python] autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 [ea-utils] release-location: https://dl.dropboxusercontent.com/u/428435/ea-utils.1.1.2-537.tar.gz
 * 1) autoconf-make-options: -j4
 * 2) autoconf-configure-options: --enable-shared --enable-unicode=ucs2 --enable-unicode=ucs4

the ea-utils program is modified and downloaded from dropbox location. Modification includes change at line 4 ("CC=g++44") in Makefile. Rest all code is same.
 * run the installation
 * python qiime-deploy/qiime-deploy.py QIIME-1.8/ -f qiime-deploy-conf/qiime-1.8.0/qiime.conf --force-remove-failed-dirs 2> install_log 1>&2

Results DEPLOYMENT SUMMARY Packages deployed successfully: data-lanemask, data-core, clearcut, raxml, ampliconnoise, blat, sourcetracker, rtax, cytoscape, chimeraslayer, python, drisee, gg_otus, infernal, vienna, ea-utils, mothur, fasttree, bwa, pplacer, blast, parsinsert, muscle, rdpclassifier, SeqPrep, r, cdhit, uclust, ape, r-color-brewer, numpy, SQLAlchemy, klar, tornado, ipython, qcli, pysqlite, gdata, vegan, random-forest, gtools, setuptools, optparse, mpi4py, pycogent, matplotlib, pynast, pprospector, MySQL-python, tax2tree, qiime, pyqi, sphinx, emperor, biom-format, qiime-galaxy, galaxy, cdbtools Packages failed to deploy: pyzmq



QIIME Links
Previous QIIME installations https://docs.uabgrid.uab.edu/wiki/QIIME_1.5 QIIME http://qiime.org/ http://qiime.org/index.html http://qiime.org/documentation_index.html Tutorials http://qiime.org/tutorials/tutorial.html http://qiime.org/tutorials/index.html http://qiime.org/tutorials/processing_illumina_data.html Scripts http://qiime.org/scripts/index.html Virtual Box http://qiime.org/install/virtual_box.html http://qiime.org/install/index.html

Mothur http://www.mothur.org/


 * For any questions email: rkumar@uab.edu