QIIME 1.5 - Revision history

Rkumar@uab.edu at 19:47, 30 May 2014

2014-05-30T19:47:57Z

← Older revision		Revision as of 19:47, 30 May 2014
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	== QIIME 1.5 ==		== QIIME 1.5 ==
			<br />
			<big>Note: This is an outdated version. The latest version of QIIME is available here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8</big>


	=== General Introduction ===		=== General Introduction ===
	[http://www.qiime.org/ 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.		[http://www.qiime.org/ 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.

Rkumar@uab.edu at 19:39, 30 May 2014

2014-05-30T19:39:50Z

← Older revision		Revision as of 19:39, 30 May 2014
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	=== Using QIIME 1.8 ===		=== Using QIIME 1.8 ===
	The details ~~are~~ here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8		The details provided here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8

	=== QIIME Links ===		=== QIIME Links ===

Rkumar@uab.edu at 19:36, 30 May 2014

2014-05-30T19:36:29Z

@@ Line 97: / Line 97: @@
 === Using QIIME 1.8 ===
-* Login to the cheaha cluster.
+The details are here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8
 === QIIME Links ===

Rkumar@uab.edu: /* Using QIIME 1.8 */

2014-05-30T16:06:48Z

Using QIIME 1.8

← Older revision		Revision as of 16:06, 30 May 2014
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	Download installation script and files		Download installation script and files
	git clone git://github.com/qiime/qiime-deploy.git		:git clone git://github.com/qiime/qiime-deploy.git
	git clone git://github.com/qiime/qiime-deploy-conf.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		:Edit the folling lines in qiime-deploy-conf/qiime-1.8.0/qiime.conf so that It looks like
	~~----------------~~
	[global]		[global]
	log-level: DEBUG		log-level: DEBUG
Line 130:		Line 130:
	[ea-utils]		[ea-utils]
	release-location: https://dl.dropboxusercontent.com/u/428435/ea-utils.1.1.2-537.tar.gz		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.		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 ===		=== QIIME Links ===

Rkumar@uab.edu: /* Using QIIME 1.8 */

2014-05-30T16:01:34Z

Using QIIME 1.8

← Older revision		Revision as of 16:01, 30 May 2014
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	:</code>		:</code>

			* 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.

	=== QIIME Links ===		=== QIIME Links ===

Rkumar@uab.edu at 15:37, 30 May 2014

2014-05-30T15:37:29Z

@@ Line 94: / Line 94: @@
 :<code>print_qiime_config.py
 :</code>
 === QIIME Links ===

Rkumar@uab.edu at 02:10, 11 September 2013

2013-09-11T02:10:48Z

@@ Line 77: / Line 77: @@
 * Everything seems working!!!
-=== Using QIIME ===
+=== 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).
@@ Line 85: / Line 85: @@
 :<code>print_qiime_config.py
 :</code>
 * For any questions you can reach me at rkumar@uab.edu

Rkumar@uab.edu at 17:24, 11 September 2012

2012-09-11T17:24:25Z

← Older revision		Revision as of 17:24, 11 September 2012
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	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 [http://qiime.org/install/ubuntu_install.html QIIME installation script for Ubuntu]. Here we want to install qiime at location /share/apps/ngs-ccts/QIIME-files-1.5		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 [http://qiime.org/install/ubuntu_install.html 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)		* login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)
	* Downloading the QIIME		* Downloading the QIIME
	:<code>cd /share/apps/ngs-ccts/QIIME-files-1.5		:<code>cd /share/apps/ngs-ccts/QIIME-files-1.5

Rkumar@uab.edu at 16:08, 10 September 2012

2012-09-10T16:08:00Z

← Older revision		Revision as of 16:08, 10 September 2012
Line 9:		Line 9:
	[http://qiime.org/tutorials/tutorial.html QIIME Tutorial]		[http://qiime.org/tutorials/tutorial.html QIIME Tutorial]

	=== Installation ~~steps~~ for Cheaha cluster ===		=== Installation notes for Cheaha cluster ===
	This installation is based on [http://qiime.org/install/ubuntu_install.html QIIME installation script for Ubuntu]. Here we want to install qiime at location /share/apps/ngs-ccts/QIIME-files-1.5		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 [http://qiime.org/install/ubuntu_install.html 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)		* login to the head node on cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)
Line 53:		Line 53:

	* QIIME installation steps		* QIIME installation steps
	:<code>module load python/python-2.7		:<code>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 mpich/mpich2-gnu
	:module load haskell/ghc		:module load haskell/ghc
	:unset DISPLAY		:unset DISPLAY
	:python app-deploy.py ~~$UABGRID_SCRATCH~~/qiime_software_1.5~~.1/~~ -f etc/qiime_1.5.0.conf		:python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf
	:</code>		:</code>

Line 84:		Line 85:
	:<code>print_qiime_config.py		:<code>print_qiime_config.py
	:</code>		:</code>
			* For any questions you can reach me at rkumar@uab.edu

Rkumar@uab.edu: /* QIIME 1.5 */

2012-09-10T15:58:03Z

QIIME 1.5

← Older revision		Revision as of 15:58, 10 September 2012
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	* Everything seems working!!!		* Everything seems working!!!

			=== Using QIIME ===

			* 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).
			:<code>source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh
			:</code>
			* QIIME is ready for usage. You can check the qiime configurations using following command
			:<code>print_qiime_config.py
			:</code>