QIIME 1.8

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Contents

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).
source /share/apps/ngs-ccts/QIIME/QIIME-files-1.8/QIIME-1.8/activate.sh
  • QIIME is ready for usage. You can check the qiime configurations using following command
print_qiime_config.py

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-make-options: -j4
#autoconf-configure-options: --enable-shared --enable-unicode=ucs2 --enable-unicode=ucs4
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

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
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