QIIME 1.5: Difference between revisions
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* Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc | * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc | ||
:<code> cd app-deploy-qiime-1.5.0/etc | :<code> cd app-deploy-qiime-1.5.0/etc</code> | ||
* Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes | * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes | ||
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set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default | 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/ | python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/ | ||
* QIIME installation steps | * QIIME installation steps | ||
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/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release | /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release | ||
* Note: | * 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!!! |
Revision as of 15:51, 10 September 2012
QIIME 1.5
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 steps for Cheaha cluster
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 head node on 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
module load python/python-2.7
- module load mpich/mpich2-gnu
- module load haskell/ghc
- unset DISPLAY
- python app-deploy.py $UABGRID_SCRATCH/qiime_software_1.5.1/ -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!!!