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Note: This is an outdated version.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


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

[global] log-level: INFO max-deploy-threads: 1 append-environment-to-bashrc: no append-environment-to-bashprofile: no
 * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes

[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-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 set-environment-variables-deploypath: LD_LIBRARY_PATH=lib
 * 1) autoconf-make-options: -j4
 * 2) autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4

[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

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


 * 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).


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

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).


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

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