QIIME 1.5

QIIME 1.5

Note: This is an outdated version. The latest version of QIIME is available here https://docs.uabgrid.uab.edu/wiki/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.

QIIME 1.5 installation files (edited for installation on Cheaha cluster) are located at /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0
QIIME 1.5 program is located at /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/
QIIME Tutorial

Installation notes for Cheaha cluster

QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section "Using QIIME". This installation is based on QIIME installation script for Ubuntu. Here we want to install qiime at location /share/apps/ngs-ccts/QIIME-files-1.5

• login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)
• Downloading the QIIME

cd /share/apps/ngs-ccts/QIIME-files-1.5

wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz

tar zxvf app-deploy-qiime-1.5.0.tgz

• Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc

cd app-deploy-qiime-1.5.0/etc

• Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes

[global]
log-level: INFO
max-deploy-threads: 1
append-environment-to-bashrc: no
append-environment-to-bashprofile: no

[python]
version: 2.7.1
build-type: autoconf
release-file-name: Python-2.7.1.tgz
release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz
relative-directory-add-to-path: bin
#autoconf-make-options: -j4
#autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4
autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2
set-environment-variables-deploypath: LD_LIBRARY_PATH=lib

[qiime]
version: 1.5.0
build-type: python-distutils
release-file-name: Qiime-1.5.0.tar.gz
release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz
relative-directory-add-to-path: bin
copy-source-to-final-deploy: yes
deps: pycogent, matplotlib
set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/
set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default
python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/

• QIIME installation steps

cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/

module load python/python-2.7

module load mpich/mpich2-gnu

module load haskell/ghc

unset DISPLAY

python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf

• At end of the installation you will see a log of modules installed like this

DEPLOYMENT SUMMARY
Packages deployed successfully:
data-lanemask, data-core, clearcut, raxml, ampliconnoise, cdbtools, rtax, cytoscape, chimeraslayer, drisee, gg_otus, infernal,     vienna, mothur, python, fasttree, pplacer, blast, parsinsert, r, muscle, rdpclassifier, cdhit, uclust, numpy, SQLAlchemy, tornado, ipython, setuptools, mpi4py, biom-format, pycogent, matplotlib, MySQL-python, sphinx, pynast, pprospector, qiime
Packages skipped (assumed successful): 

Packages failed to deploy:
pyzmq 

Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:
/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release

• Note: For some reason the file .qiime_config_default was created in my home directory which I later moved to location /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/

• Everything seems working!!!

Using QIIME 1.5

• 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-files-1.5/qiime_software_1.5/activate.sh

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

print_qiime_config.py

Using QIIME 1.7

• 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-files-1.7/QIIME-1.7/activate.sh

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

print_qiime_config.py

Using QIIME 1.8

The details provided here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8

QIIME Links

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 you can reach me at rkumar@uab.edu