https://docs.uabgrid.uab.edu/w/api.php?action=feedcontributions&feedformat=atom&user=Rkumar%40uab.edu 2026-04-20T05:05:17Z User contributions MediaWiki 1.38.2 https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4781 2014-05-30T19:47:57Z

<p>Rkumar@uab.edu: </p> <hr /> <div><br /> <br /> <br /> == QIIME 1.5 ==<br /> &lt;br /&gt;<br /> &lt;big&gt;Note: This is an outdated version. The latest version of QIIME is available here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8&lt;/big&gt;<br /> <br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME 1.5 ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> === Using QIIME 1.7 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.7/QIIME-1.7/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> <br /> === Using QIIME 1.8 ===<br /> The details provided here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8<br /> <br /> === QIIME Links ===<br /> QIIME<br /> http://qiime.org/<br /> http://qiime.org/index.html<br /> http://qiime.org/documentation_index.html<br /> <br /> Tutorials<br /> http://qiime.org/tutorials/tutorial.html<br /> http://qiime.org/tutorials/index.html<br /> http://qiime.org/tutorials/processing_illumina_data.html<br /> <br /> Scripts<br /> http://qiime.org/scripts/index.html<br /> <br /> Virtual Box<br /> http://qiime.org/install/virtual_box.html<br /> http://qiime.org/install/index.html<br /> <br /> Mothur<br /> http://www.mothur.org/<br /> <br /> <br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4780 2014-05-30T19:39:50Z

<p>Rkumar@uab.edu: </p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME 1.5 ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> === Using QIIME 1.7 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.7/QIIME-1.7/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> <br /> === Using QIIME 1.8 ===<br /> The details provided here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8<br /> <br /> === QIIME Links ===<br /> QIIME<br /> http://qiime.org/<br /> http://qiime.org/index.html<br /> http://qiime.org/documentation_index.html<br /> <br /> Tutorials<br /> http://qiime.org/tutorials/tutorial.html<br /> http://qiime.org/tutorials/index.html<br /> http://qiime.org/tutorials/processing_illumina_data.html<br /> <br /> Scripts<br /> http://qiime.org/scripts/index.html<br /> <br /> Virtual Box<br /> http://qiime.org/install/virtual_box.html<br /> http://qiime.org/install/index.html<br /> <br /> Mothur<br /> http://www.mothur.org/<br /> <br /> <br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4779 2014-05-30T19:36:29Z

<p>Rkumar@uab.edu: </p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME 1.5 ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> === Using QIIME 1.7 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.7/QIIME-1.7/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> <br /> === Using QIIME 1.8 ===<br /> The details are here https://docs.uabgrid.uab.edu/wiki/QIIME_1.8<br /> <br /> === QIIME Links ===<br /> QIIME<br /> http://qiime.org/<br /> http://qiime.org/index.html<br /> http://qiime.org/documentation_index.html<br /> <br /> Tutorials<br /> http://qiime.org/tutorials/tutorial.html<br /> http://qiime.org/tutorials/index.html<br /> http://qiime.org/tutorials/processing_illumina_data.html<br /> <br /> Scripts<br /> http://qiime.org/scripts/index.html<br /> <br /> Virtual Box<br /> http://qiime.org/install/virtual_box.html<br /> http://qiime.org/install/index.html<br /> <br /> Mothur<br /> http://www.mothur.org/<br /> <br /> <br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.8&diff=4778 2014-05-30T19:35:02Z

<p>Rkumar@uab.edu: Created page with &quot; == QIIME 1.8 == === General Introduction === [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open sou...&quot;</p> <hr /> <div><br /> == QIIME 1.8 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> === Using QIIME 1.8 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME/QIIME-files-1.8/QIIME-1.8/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> Installation notes<br /> Make following changes first<br /> module load python/python-2.7<br /> module load mpich/mpich2-gnu<br /> module load haskell/ghc<br /> unset DISPLAY<br /> <br /> Download installation script and files<br /> git clone git://github.com/qiime/qiime-deploy.git<br /> git clone git://github.com/qiime/qiime-deploy-conf.git<br /> <br /> Edit the folling lines in qiime-deploy-conf/qiime-1.8.0/qiime.conf so that It looks like<br /> <br /> [global]<br /> log-level: DEBUG<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: yes<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> <br /> [ea-utils]<br /> release-location: https://dl.dropboxusercontent.com/u/428435/ea-utils.1.1.2-537.tar.gz<br /> <br /> the ea-utils program is modified and downloaded from dropbox location. Modification includes change at line 4 (&quot;CC=g++44&quot;) in Makefile. Rest all code is same.<br /> :run the installation<br /> :python qiime-deploy/qiime-deploy.py QIIME-1.8/ -f qiime-deploy-conf/qiime-1.8.0/qiime.conf --force-remove-failed-dirs 2&gt; install_log 1&gt;&amp;2<br /> <br /> Results<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> <br /> Packages failed to deploy:<br /> pyzmq<br /> <br /> ***<br /> <br /> === QIIME Links ===<br /> <br /> Previous QIIME installations<br /> https://docs.uabgrid.uab.edu/wiki/QIIME_1.5<br /> <br /> QIIME<br /> http://qiime.org/<br /> http://qiime.org/index.html<br /> http://qiime.org/documentation_index.html<br /> <br /> Tutorials<br /> http://qiime.org/tutorials/tutorial.html<br /> http://qiime.org/tutorials/index.html<br /> http://qiime.org/tutorials/processing_illumina_data.html<br /> <br /> Scripts<br /> http://qiime.org/scripts/index.html<br /> <br /> Virtual Box<br /> http://qiime.org/install/virtual_box.html<br /> http://qiime.org/install/index.html<br /> <br /> Mothur<br /> http://www.mothur.org/<br /> <br /> <br /> * For any questions email: rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4777 2014-05-30T16:06:48Z

<p>Rkumar@uab.edu: /* Using QIIME 1.8 */</p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME 1.5 ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> === Using QIIME 1.7 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.7/QIIME-1.7/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> <br /> === Using QIIME 1.8 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME/QIIME-files-1.8/QIIME-1.8/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> * Installation notes<br /> Make following changes first<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> <br /> Download installation script and files<br /> :git clone git://github.com/qiime/qiime-deploy.git<br /> :git clone git://github.com/qiime/qiime-deploy-conf.git<br /> :Edit the folling lines in qiime-deploy-conf/qiime-1.8.0/qiime.conf so that It looks like<br /> <br /> [global]<br /> log-level: DEBUG<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: yes<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> <br /> [ea-utils]<br /> release-location: https://dl.dropboxusercontent.com/u/428435/ea-utils.1.1.2-537.tar.gz<br /> <br /> the ea-utils program is modified and downloaded from dropbox location. Modification includes change at line 4 (&quot;CC=g++44&quot;) in Makefile. Rest all code is same.<br /> :run the installation<br /> :python qiime-deploy/qiime-deploy.py QIIME-1.8/ -f qiime-deploy-conf/qiime-1.8.0/qiime.conf --force-remove-failed-dirs 2&gt; install_log 1&gt;&amp;2<br /> <br /> Results<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> <br /> Packages failed to deploy:<br /> pyzmq<br /> <br /> ***<br /> <br /> === QIIME Links ===<br /> QIIME<br /> http://qiime.org/<br /> http://qiime.org/index.html<br /> http://qiime.org/documentation_index.html<br /> <br /> Tutorials<br /> http://qiime.org/tutorials/tutorial.html<br /> http://qiime.org/tutorials/index.html<br /> http://qiime.org/tutorials/processing_illumina_data.html<br /> <br /> Scripts<br /> http://qiime.org/scripts/index.html<br /> <br /> Virtual Box<br /> http://qiime.org/install/virtual_box.html<br /> http://qiime.org/install/index.html<br /> <br /> Mothur<br /> http://www.mothur.org/<br /> <br /> <br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4776 2014-05-30T16:01:34Z

<p>Rkumar@uab.edu: /* Using QIIME 1.8 */</p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME 1.5 ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> === Using QIIME 1.7 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.7/QIIME-1.7/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> <br /> === Using QIIME 1.8 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME/QIIME-files-1.8/QIIME-1.8/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> * Installation notes<br /> Make following changes first<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> <br /> Download installation script and files<br /> git clone git://github.com/qiime/qiime-deploy.git<br /> git clone git://github.com/qiime/qiime-deploy-conf.git<br /> Edit the folling lines in qiime-deploy-conf/qiime-1.8.0/qiime.conf so that It looks like<br /> ----------------<br /> [global]<br /> log-level: DEBUG<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: yes<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> <br /> [ea-utils]<br /> release-location: https://dl.dropboxusercontent.com/u/428435/ea-utils.1.1.2-537.tar.gz<br /> ---------------------<br /> the ea-utils program is modified and downloaded from dropbox location. Modification includes change at line 4 (&quot;CC=g++44&quot;) in Makefile. Rest all code is same.<br /> <br /> === QIIME Links ===<br /> QIIME<br /> http://qiime.org/<br /> http://qiime.org/index.html<br /> http://qiime.org/documentation_index.html<br /> <br /> Tutorials<br /> http://qiime.org/tutorials/tutorial.html<br /> http://qiime.org/tutorials/index.html<br /> http://qiime.org/tutorials/processing_illumina_data.html<br /> <br /> Scripts<br /> http://qiime.org/scripts/index.html<br /> <br /> Virtual Box<br /> http://qiime.org/install/virtual_box.html<br /> http://qiime.org/install/index.html<br /> <br /> Mothur<br /> http://www.mothur.org/<br /> <br /> <br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4775 2014-05-30T15:37:29Z

<p>Rkumar@uab.edu: </p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME 1.5 ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> === Using QIIME 1.7 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.7/QIIME-1.7/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> <br /> === Using QIIME 1.8 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME/QIIME-files-1.8/QIIME-1.8/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> <br /> === QIIME Links ===<br /> QIIME<br /> http://qiime.org/<br /> http://qiime.org/index.html<br /> http://qiime.org/documentation_index.html<br /> <br /> Tutorials<br /> http://qiime.org/tutorials/tutorial.html<br /> http://qiime.org/tutorials/index.html<br /> http://qiime.org/tutorials/processing_illumina_data.html<br /> <br /> Scripts<br /> http://qiime.org/scripts/index.html<br /> <br /> Virtual Box<br /> http://qiime.org/install/virtual_box.html<br /> http://qiime.org/install/index.html<br /> <br /> Mothur<br /> http://www.mothur.org/<br /> <br /> <br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4655 2013-09-11T02:10:48Z

<p>Rkumar@uab.edu: </p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME 1.5 ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> === Using QIIME 1.7 ===<br /> * Login to the cheaha cluster.<br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.7/QIIME-1.7/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> <br /> === QIIME Links ===<br /> QIIME<br /> http://qiime.org/<br /> http://qiime.org/index.html<br /> http://qiime.org/documentation_index.html<br /> <br /> Tutorials<br /> http://qiime.org/tutorials/tutorial.html<br /> http://qiime.org/tutorials/index.html<br /> http://qiime.org/tutorials/processing_illumina_data.html<br /> <br /> Scripts<br /> http://qiime.org/scripts/index.html<br /> <br /> Virtual Box<br /> http://qiime.org/install/virtual_box.html<br /> http://qiime.org/install/index.html<br /> <br /> Mothur<br /> http://www.mothur.org/<br /> <br /> <br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=NgsCctsBuildVelvet&diff=4563 2013-07-09T19:51:58Z

<p>Rkumar@uab.edu: </p> <hr /> <div>NOTE: it is possible to build Velvet to support &gt; 1 threads: http://www.dolphing.com/re-velvet-users-velvet-1-1-01-multithreading-17<br /> * add OPENMP=1 to Makefile (or 'OPENMP=1' argument to make)<br /> * update galaxy/tools/sr_assembly/velvet*_wrapper.py to set OMP_NUM_THREADS=''N-1'' &amp; OMP_THREAD_LIMIT=''N-1''<br /> * update galaxy/universe_wsgi.ini.sanitized to add -pe smp ''N''<br /> <br /> Current build:<br /> <br /> TARGET_VER=velvet_1.2.08<br /> wget http://www.ebi.ac.uk/~zerbino/velvet/${TARGET_VER}.tgz<br /> tar xzvf ${TARGET_VER}.tgz<br /> rm ${TARGET_VER}.tgz<br /> cd ${TARGET_VER}<br /> <br /> Edit Makefile to change max k mer available or supply the values at the build time as commandline arguments.<br /> <br /> vi Makefile<br /> /MAXKMER<br /> $bcw57<br /> LONGSEQUENCES=true<br /> :wq<br /> <br /> Build<br /> <br /> make<br /> or<br /> make 'OPENMP=1' 'CATEGORIES=3' 'MAXKMERLENGTH=50' (using commandline arguments)<br /> <br /> done</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=R-packages&diff=4358 2013-01-14T19:17:12Z

<p>Rkumar@uab.edu: Created page with &quot; == R-packages - A central location for external R packages. == The path for dicrectory is ''''''/share/apps/ngs-ccts/R_packages/'''''' Example for installing a package nam...&quot;</p> <hr /> <div><br /> == R-packages - A central location for external R packages. ==<br /> <br /> The path for dicrectory is <br /> ''''''/share/apps/ngs-ccts/R_packages/''''''<br /> <br /> Example for installing a package named &quot;HMP&quot;<br /> module load R/R-2.15.0 # load an appropriate R module<br /> export R_LIBS=/share/apps/ngs-ccts/R_packages/ #export a environment variable which have the path for R library<br /> R #launch R<br /> install.packages(&quot;HMP&quot;) #to install library HMP<br /> library(&quot;HMP&quot;) #to load library HMP<br /> <br /> Example for using a library HMP (if already installed)<br /> module load R/R-2.15.0 # load an appropriate R module<br /> export R_LIBS=/share/apps/ngs-ccts/R_packages/ #export a environment variable which have the path for R library<br /> Inside R<br /> library(&quot;HMP&quot;) #to load library HMP</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=NgsCcts&diff=4357 2013-01-14T19:08:13Z

<p>Rkumar@uab.edu: </p> <hr /> <div>= Shared CCTS NGS apps =<br /> <br /> This page documents apps installed by the CCTS BMI group in cheaha:/share/apps/ngs-ccts<br /> <br /> Links to latest versions of each package are in /share/apps/ngs-ccts/latest.<br /> <br /> See also [[PublicDatasetsNgs]] for genomes, indices and databases <br /> <br /> == Microbiome == <br /> * [[QIIME 1.5]]<br /> <br /> == R-packages == <br /> * [[R-packages]]<br /> <br /> == Alignment Visualization ==<br /> * [http://www.broadinstitute.org/software/igv/download IGV]<br /> ** [http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.1.7.zip IGV 2.1.23]<br /> * [http://www.broadinstitute.org/software/igv/download igvtools] <br /> ** [http://www.broadinstitute.org/igv/projects/downloads/igvtools_2.1.7.zip IGVtools 2.1.7]<br /> <br /> == Short Read Aligners ==<br /> * [ tophat]<br /> ** tophat-2.0.6 [http://tophat.cbcb.umd.edu/downloads/tophat-2.0.6.Linux_x86_64.tar.gz (binary)]<br /> * [http://bowtie-bio.sourceforge.net bowtie]<br /> ** bowtie-0.12.7 (linked from Galaxy)<br /> ** bowtie-0.12.8 [http://downloads.sourceforge.net/project/bowtie-bio/bowtie/0.12.8/bowtie-0.12.8-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie%2F0.12.8%2F (binary)]<br /> * [http://bowtie-bio.sourceforge.net/bowtie2 bowtie2]<br /> ** bowtie2-2.0.0-beta7 [http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.0.0-beta7/bowtie2-2.0.0-beta7-linux-x86_64.zip?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbowtie-bio%2Ffiles%2Fbowtie2%2F2.0.0-beta7%2F&amp;ts=1349813862&amp;use_mirror=superb-dca3 (download binary)]<br /> * bwa <br /> ** bwa-0.6.2 [http://downloads.sourceforge.net/project/bio-bwa/bwa-0.6.2.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fbio-bwa%2Ffiles%2F&amp;ts=1349814953&amp;use_mirror=iweb (download src)] [[NgsCctsBuildBwa]]<br /> <br /> == Short Read (denovo) Assemblers ==<br /> * [http://www.ebi.ac.uk/~zerbino/velvet velvet ]<br /> ** velvet_1.2.08 ([http://www.ebi.ac.uk/~zerbino/velvet/velvet_1.2.08.tgz download src])([[NgsCctsBuildVelvet]])<br /> *** MAXKMERLENGTH = 57<br /> *** LONGSEQUENCES<br /> === in process ===<br /> * [http://www.bcgsc.ca/platform/bioinfo/software/abyss ABySS] '''NOT DONE'''<br /> ** abyss_1.3.4 ([http://www.bcgsc.ca/downloads/abyss/abyss-1.3.4.tar.gz download src])([[NgsCctsBuildAbyss]])<br /> *** maxk=100<br /> * [http://www.broadinstitute.org/scientific-community/science/projects/viral-genomics/viral-genomics-analysis-software?package=VICUNA VICUNA] from Broad Institute - Viral genome denovo assembler '''NOT DONE'''<br /> ** VICUNA_v1.2 [http://www.broadinstitute.org/software/viral/vicuna/vicuna.zip]<br /> ** V-FAT [http://www.broadinstitute.org/software/viral/vfat/vfat.zip]<br /> ** V-Phaser &amp; V-Profiler [http://www.broadinstitute.org/software/viral/v_phaser/v_phaser.zip]</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4252 2012-09-11T17:24:25Z

<p>Rkumar@uab.edu: </p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4251 2012-09-10T16:08:00Z

<p>Rkumar@uab.edu: </p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation notes for Cheaha cluster ===<br /> QIIME is already installed on Cheaha cluster. If you just want to use QIIME, go to the next section &quot;Using QIIME&quot;. 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<br /> <br /> * login to the head node on cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5/app-deploy-qiime-1.5.0/<br /> :module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5 -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;<br /> * For any questions you can reach me at rkumar@uab.edu</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4250 2012-09-10T15:58:03Z

<p>Rkumar@uab.edu: /* QIIME 1.5 */</p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation steps for Cheaha cluster ===<br /> 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<br /> <br /> * login to the head node on cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py $UABGRID_SCRATCH/qiime_software_1.5.1/ -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!<br /> <br /> === Using QIIME ===<br /> <br /> * 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).<br /> :&lt;code&gt;source /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/activate.sh<br /> :&lt;/code&gt;<br /> * QIIME is ready for usage. You can check the qiime configurations using following command<br /> :&lt;code&gt;print_qiime_config.py<br /> :&lt;/code&gt;</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4249 2012-09-10T15:51:28Z

<p>Rkumar@uab.edu: /* Installation steps for Cheaha cluster */</p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation steps for Cheaha cluster ===<br /> 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<br /> <br /> * login to the head node on cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc&lt;/code&gt;<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py $UABGRID_SCRATCH/qiime_software_1.5.1/ -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * 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/<br /> <br /> * Everything seems working!!!</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4248 2012-09-10T15:44:46Z

<p>Rkumar@uab.edu: /* Installation steps for Cheaha cluster */</p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation steps for Cheaha cluster ===<br /> 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<br /> <br /> * login to the head node on cheaha cluster and make sure no external module is loaded (for avoiding any possible conflicts)<br /> * Downloading the QIIME <br /> :&lt;code&gt;cd /share/apps/ngs-ccts/QIIME-files-1.5<br /> :wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> :tar zxvf app-deploy-qiime-1.5.0.tgz<br /> :&lt;/code&gt;<br /> <br /> * Open the configuration file qiime_1.5.0.conf located at app-deploy-qiime-1.5.0/etc<br /> :&lt;code&gt; cd app-deploy-qiime-1.5.0/etc<br /> <br /> * Edit the portion of configuration file qiime_1.5.0.conf to reflect these changes<br /> [global]<br /> log-level: INFO<br /> max-deploy-threads: 1<br /> append-environment-to-bashrc: no<br /> append-environment-to-bashprofile: no<br /> <br /> [python]<br /> version: 2.7.1<br /> build-type: autoconf<br /> release-file-name: Python-2.7.1.tgz<br /> release-location: ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/Python-2.7.1.tgz<br /> relative-directory-add-to-path: bin<br /> #autoconf-make-options: -j4<br /> #autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2 --enable-unicode=ucs4<br /> autoconf-configure-options: --enable-shared --with-zlib=/usr/include --enable-unicode=ucs2<br /> set-environment-variables-deploypath: LD_LIBRARY_PATH=lib<br /> <br /> [qiime]<br /> version: 1.5.0<br /> build-type: python-distutils<br /> release-file-name: Qiime-1.5.0.tar.gz<br /> release-location: http://sourceforge.net/projects/qiime/files/releases/Qiime-1.5.0.tar.gz<br /> relative-directory-add-to-path: bin<br /> copy-source-to-final-deploy: yes<br /> deps: pycogent, matplotlib<br /> set-environment-variables-deploypath: QIIME=./,PYTHONPATH=lib/<br /> set-environment-variables-value: QIIME_CONFIG_FP=/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/.qiime_config_default<br /> python-install-options: --install-scripts=bin/ --install-purelib=lib/ --install-data=lib/<br /> <br /> <br /> * QIIME installation steps<br /> :&lt;code&gt;module load python/python-2.7<br /> :module load mpich/mpich2-gnu<br /> :module load haskell/ghc<br /> :unset DISPLAY<br /> :python app-deploy.py $UABGRID_SCRATCH/qiime_software_1.5.1/ -f etc/qiime_1.5.0.conf<br /> :&lt;/code&gt;<br /> <br /> * At end of the installation you will see a log of modules installed like this<br /> DEPLOYMENT SUMMARY<br /> Packages deployed successfully:<br /> 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<br /> Packages skipped (assumed successful): <br /> <br /> Packages failed to deploy:<br /> pyzmq <br /> <br /> Directories of failed applications must be removed manually or --force-remove-failed-dirs must be specified:<br /> /share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/pyzmq-2.1.9-release<br /> <br /> * Note: for some reason a file .</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4247 2012-09-10T15:07:31Z

<p>Rkumar@uab.edu: /* QIIME 1.5 */</p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation steps for Cheaha cluster ===<br /> This installation is based on [http://qiime.org/install/ubuntu_install.html QIIME installation script for Ubuntu].<br /> <br /> # Make sure no external module is loaded (for avoiding any conflicts)<br /> # Downloading the QIIME <br /> &lt;source lang=&quot;csharp&quot;&gt;wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/app-deploy-qiime-1.5.0.tgz<br /> tar zxvf app-deploy-qiime-1.5.0.tgz<br /> &lt;/source&gt;<br /> # Editing the configuration file</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=QIIME_1.5&diff=4246 2012-09-10T14:30:13Z

<p>Rkumar@uab.edu: Created page with &quot; == QIIME 1.5 == === General Introduction === [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) stands for Quantitative Insights Into Microbial Ecology. QIIME is an open sou...&quot;</p> <hr /> <div><br /> == QIIME 1.5 ==<br /> <br /> === General Introduction ===<br /> [http://www.qiime.org/ QIIME] (pronounced &quot;chime&quot;) 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. <br /> <br /> 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''' &lt;br/&gt;<br /> QIIME 1.5 program is located at '''/share/apps/ngs-ccts/QIIME-files-1.5/qiime_software_1.5/''' &lt;br/&gt;<br /> [http://qiime.org/tutorials/tutorial.html QIIME Tutorial]<br /> <br /> === Installation steps for Cheaha cluster ===</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=NgsCcts&diff=4245 2012-09-10T14:24:22Z

<p>Rkumar@uab.edu: </p> <hr /> <div>= Shared CCTS NGS apps =<br /> <br /> This page documents apps installed by the CCTS BMI group in cheaha:/share/apps/ngs-ccts<br /> <br /> * [[QIIME 1.5]]</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=Intermine&diff=3531 2012-01-07T22:54:42Z

<p>Rkumar@uab.edu: /* Installation notes for Intermine on Ubuntu 64bit */</p> <hr /> <div>== Motivation ==<br /> <br /> CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service. <br /> <br /> <br /> == Web Resources for Intermine == <br /> <br /> * Home page http://www.intermine.org/<br /> <br /> * About Intermine http://intermine.org/wiki/InterMine<br /> <br /> * Intermine Overview http://intermine.org/wiki/InterMineOverview<br /> <br /> * Prerequisite and downloading http://intermine.org/wiki/GettingStarted http://intermine.org/wiki/Prerequisites<br /> <br /> * Hardware requirements http://intermine.org/wiki/Hardware<br /> <br /> * QuickStart http://intermine.org/wiki/QuickStart<br /> <br /> * TroubleShooting http://intermine.org/wiki/TroubleshootingTips<br /> <br /> * Download/Get intermine http://intermine.org/wiki/SVNCheckout<br /> <br /> * Intermine use cases http://intermine.org/wiki/InterMineUseCases<br /> <br /> <br /> <br /> ==Examples of databases using Intermine ==<br /> <br /> * RatMine: http://ratmine.mcw.edu/<br /> * modENCODE: http://www.modencode.org/<br /> * Flymine: http://www.flymine.org/<br /> * Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do<br /> * Targetmine : http://targetmine.nibio.go.jp/<br /> * Metabolicmine : http://www.metabolicmine.org/<br /> <br /> <br /> <br /> <br /> == Installation notes for Intermine on Ubuntu 64bit==<br /> <br /> <br /> <br /> <br /> Step A: Install all prerequistite tools required for Intermine installation<br /> <br /> The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites<br /> <br /> '''Additional install notes''' . This Installation is done on a Virtual box (running on win 7 64bits).<br /> <br /> 1. Install subversion <br /> sudo apt-get install subversion<br /> <br /> 2. Install sunjava6jdk<br /> sudo add-apt-repository &quot;deb http://archive.canonical.com/ lucid partner&quot; (added a source repository)<br /> Or add following to the /etc/apt/osurcelist<br /> deb http://archive.canonical.com/ubuntu lucid partner<br /> deb-src http://archive.canonical.com/ubuntu lucid partner<br /> Commands to run - <br /> sudo apt-get update<br /> sudo apt-get install sun-java6-jdk<br /> <br /> 3. Install ant<br /> a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/<br /> b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26<br /> c. export ANT_HOME=/home/ranjit/ant (ant is in my home directory)<br /> d. export PATH=${PATH}:${ANT_HOME}/bin<br /> These variable can be included in a batch script which automatically runs after system login. <br /> <br /> 4. Install Tomcat <br /> Download tomcat, unzip it and place it at a location you know.<br /> Just start/stop the server as (ant is in my home directory)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) <br /> Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml ($CATALINA_HOME is the installation directory)<br /> &lt;tomcat-users&gt;<br /> &lt;!-- you can add more users or roles if needed --&gt;<br /> &lt;role rolename=&quot;manager&quot;/&gt;<br /> &lt;user username=&quot;manager&quot; password=&quot;manager&quot; roles=&quot;manager&quot;/&gt;<br /> &lt;/tomcat-users&gt;<br /> <br /> Add java memmory requirements<br /> To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR<br /> Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell: export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”<br /> If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.<br /> <br /> 5. Install postgresql 8.4<br /> sudo apt-get install postgresql-8.4<br /> Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites<br /> sudo vim /etc/postgresql/8.4/main/postgresql.conf<br /> Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)<br /> Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf to use &quot;md5&quot; MD5 authentication<br /> sudo /etc/init.d/postgresql-8.4 restart (restart the server)<br /> <br /> Install Bioseg into postgres<br /> sudo apt-get install postgresql-contrib-8.4<br /> sudo apt-get install postgresql-server-dev-8.4<br /> Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ <br /> Unzip and Install it as<br /> make USE_PGXS=t clean<br /> make USE_PGXS=t<br /> make USE_PGXS=t install<br /> <br /> When a database is created it can be added to it by<br /> psql (database) &lt;bioseg.sql<br /> psql (database) &lt;btree_gist.sql<br /> To start/stop/restart postgressql do..<br /> sudo /etc/init.d/postgresql-8.4 start (replace start with stop/restart)<br /> <br /> 6.Install Junit<br /> Download from http://www.junit.org/<br /> Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)<br /> Add to the java classpath with this command, replacing X.X with the version number.<br /> like<br /> export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar<br /> <br /> <br /> <br /> Step B: Download and Install Intermine<br /> svn co svn://subversion.flymine.org/branches/intermine_0_98<br /> Thats all :)<br /> <br /> Step C: Creating a example database using Malaria called Malariamine.<br /> Please follow the steps given at http://intermine.org/wiki/GettingStarted</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=Intermine&diff=3530 2012-01-07T22:53:37Z

<p>Rkumar@uab.edu: </p> <hr /> <div>== Motivation ==<br /> <br /> CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service. <br /> <br /> <br /> == Web Resources for Intermine == <br /> <br /> * Home page http://www.intermine.org/<br /> <br /> * About Intermine http://intermine.org/wiki/InterMine<br /> <br /> * Intermine Overview http://intermine.org/wiki/InterMineOverview<br /> <br /> * Prerequisite and downloading http://intermine.org/wiki/GettingStarted http://intermine.org/wiki/Prerequisites<br /> <br /> * Hardware requirements http://intermine.org/wiki/Hardware<br /> <br /> * QuickStart http://intermine.org/wiki/QuickStart<br /> <br /> * TroubleShooting http://intermine.org/wiki/TroubleshootingTips<br /> <br /> * Download/Get intermine http://intermine.org/wiki/SVNCheckout<br /> <br /> * Intermine use cases http://intermine.org/wiki/InterMineUseCases<br /> <br /> <br /> <br /> ==Examples of databases using Intermine ==<br /> <br /> * RatMine: http://ratmine.mcw.edu/<br /> * modENCODE: http://www.modencode.org/<br /> * Flymine: http://www.flymine.org/<br /> * Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do<br /> * Targetmine : http://targetmine.nibio.go.jp/<br /> * Metabolicmine : http://www.metabolicmine.org/<br /> <br /> <br /> <br /> <br /> == Installation notes for Intermine on Ubuntu 64bit==<br /> <br /> <br /> <br /> <br /> Step A: Install all prerequistite tools required for Intermine installation<br /> <br /> The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites<br /> <br /> '''Additional install notes''' . This Installation is done on a Virtual box (running on win 7 64bits).<br /> <br /> 1. Install subversion <br /> sudo apt-get install subversion<br /> <br /> 2. Install sunjava6jdk<br /> sudo add-apt-repository &quot;deb http://archive.canonical.com/ lucid partner&quot; (added a source repository)<br /> Or add following to the /etc/apt/osurcelist<br /> deb http://archive.canonical.com/ubuntu lucid partner<br /> deb-src http://archive.canonical.com/ubuntu lucid partner<br /> Commands to run - <br /> sudo apt-get update<br /> sudo apt-get install sun-java6-jdk<br /> <br /> 3. Install ant<br /> a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/<br /> b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26<br /> c. export ANT_HOME=/home/ranjit/ant (ant is in my home directory)<br /> d. export PATH=${PATH}:${ANT_HOME}/bin<br /> These variable can be included in a batch script which automatically runs after system login. <br /> <br /> 4. Install Tomcat <br /> Download tomcat, unzip it and place it at a location you know.<br /> Just start/stop the server as (ant is in my home directory)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) <br /> Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml ($CATALINA_HOME is the installation directory)<br /> &lt;tomcat-users&gt;<br /> &lt;!-- you can add more users or roles if needed --&gt;<br /> &lt;role rolename=&quot;manager&quot;/&gt;<br /> &lt;user username=&quot;manager&quot; password=&quot;manager&quot; roles=&quot;manager&quot;/&gt;<br /> &lt;/tomcat-users&gt;<br /> <br /> Add java memmory requirements<br /> To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR<br /> Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell: export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”<br /> If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.<br /> <br /> 5. Install postgresql 8.4<br /> sudo apt-get install postgresql-8.4<br /> Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites<br /> sudo vim /etc/postgresql/8.4/main/postgresql.conf<br /> Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)<br /> Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf to use &quot;md5&quot; MD5 authentication<br /> sudo /etc/init.d/postgresql-8.4 restart (restart the server)<br /> <br /> Install Bioseg into postgres<br /> sudo apt-get install postgresql-contrib-8.4<br /> sudo apt-get install postgresql-server-dev-8.4<br /> Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ <br /> Unzip and Install it as<br /> make USE_PGXS=t clean<br /> make USE_PGXS=t<br /> make USE_PGXS=t install<br /> <br /> When a database is created it can be added to it by<br /> psql (database) &lt;bioseg.sql<br /> psql (database) &lt;btree_gist.sql<br /> To start/stop/restart postgressql do..<br /> sudo /etc/init.d/postgresql-8.4 start (replace start with stop/restart)<br /> <br /> 6.Install Junit<br /> Download from http://www.junit.org/<br /> Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)<br /> Add to the java classpath with this command, replacing X.X with the version number.<br /> like<br /> export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar<br /> <br /> <br /> <br /> Step B: Download and Install Intermine<br /> svn co svn://subversion.flymine.org/branches/intermine_0_98<br /> Thats all :)<br /> <br /> Step C: Creating a example database using MAlaria called Malariamine.<br /> Please follow the steps given at http://intermine.org/wiki/GettingStarted</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=Intermine&diff=3529 2012-01-07T22:48:02Z

<p>Rkumar@uab.edu: </p> <hr /> <div>== Motivation ==<br /> <br /> CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service. <br /> <br /> <br /> == Web Resources for Intermine == <br /> <br /> * Home page http://www.intermine.org/<br /> <br /> * About Intermine http://intermine.org/wiki/InterMine<br /> <br /> * Intermine Overview http://intermine.org/wiki/InterMineOverview<br /> <br /> * Prerequisite and downloading http://intermine.org/wiki/GettingStarted http://intermine.org/wiki/Prerequisites<br /> <br /> * Hardware requirements http://intermine.org/wiki/Hardware<br /> <br /> * QuickStart http://intermine.org/wiki/QuickStart<br /> <br /> * TroubleShooting http://intermine.org/wiki/TroubleshootingTips<br /> <br /> * Download/Get intermine http://intermine.org/wiki/SVNCheckout<br /> <br /> * Intermine use cases http://intermine.org/wiki/InterMineUseCases<br /> <br /> <br /> <br /> ==Examples of databases using Intermine ==<br /> <br /> * RatMine: http://ratmine.mcw.edu/<br /> * modENCODE: http://www.modencode.org/<br /> * Flymine: http://www.flymine.org/<br /> * Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do<br /> * Targetmine : http://targetmine.nibio.go.jp/<br /> * Metabolicmine : http://www.metabolicmine.org/<br /> <br /> <br /> <br /> <br /> == Installation notes for Intermine on Ubuntu 64bit==<br /> <br /> <br /> <br /> <br /> Step A: Install all prerequistite tools required for Intermine installation<br /> <br /> The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites<br /> <br /> '''Additional install notes''' . This Installation is done on a Virtual box (running on win 7 64bits).<br /> <br /> 1. Install subversion <br /> sudo apt-get install subversion<br /> <br /> 2. Install sunjava6jdk<br /> sudo add-apt-repository &quot;deb http://archive.canonical.com/ lucid partner&quot; (added a source repository)<br /> Or add following to the /etc/apt/osurcelist<br /> deb http://archive.canonical.com/ubuntu lucid partner<br /> deb-src http://archive.canonical.com/ubuntu lucid partner<br /> Commands to run - <br /> sudo apt-get update<br /> sudo apt-get install sun-java6-jdk<br /> <br /> 3. Install ant<br /> a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/<br /> b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26<br /> c. export ANT_HOME=/home/ranjit/ant (ant is in my home directory)<br /> d. export PATH=${PATH}:${ANT_HOME}/bin<br /> These variable can be included in a batch script which automatically runs after system login. <br /> <br /> 4. Install Tomcat <br /> Download tomcat, unzip it and place it at a location you know.<br /> Just start/stop the server as (ant is in my home directory)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) <br /> Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml ($CATALINA_HOME is the installation directory)<br /> &lt;tomcat-users&gt;<br /> &lt;!-- you can add more users or roles if needed --&gt;<br /> &lt;role rolename=&quot;manager&quot;/&gt;<br /> &lt;user username=&quot;manager&quot; password=&quot;manager&quot; roles=&quot;manager&quot;/&gt;<br /> &lt;/tomcat-users&gt;<br /> <br /> Add java memmory requirements<br /> To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR<br /> Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell: export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”<br /> If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.<br /> <br /> 5. Install postgresql 8.4<br /> sudo apt-get install postgresql-8.4<br /> Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites<br /> sudo vim /etc/postgresql/8.4/main/postgresql.conf<br /> Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)<br /> Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf to use &quot;md5&quot; MD5 authentication<br /> sudo /etc/init.d/postgresql-8.4 restart (restart the server)<br /> <br /> Install Bioseg into postgres<br /> sudo apt-get install postgresql-contrib-8.4<br /> sudo apt-get install postgresql-server-dev-8.4<br /> Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ <br /> Unzip and Install it as<br /> make USE_PGXS=t clean<br /> make USE_PGXS=t<br /> make USE_PGXS=t install<br /> <br /> When a database is created it can be added to it by<br /> psql (database) &lt;bioseg.sql<br /> psql (database) &lt;btree_gist.sql<br /> To start/stop/restart postgressql do..<br /> sudo /etc/init.d/postgresql-8.4 start (replace start with stop/restart)<br /> <br /> 6.Install Junit<br /> Download from http://www.junit.org/<br /> Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)<br /> Add to the java classpath with this command, replacing X.X with the version number.<br /> like<br /> export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar<br /> <br /> <br /> <br /> ----</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=Intermine&diff=3528 2012-01-07T22:47:37Z

<p>Rkumar@uab.edu: /* Examples of Inermine databases (active) */</p> <hr /> <div>== Motivation ==<br /> <br /> CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service. <br /> <br /> <br /> == Web Resources for Intermine == <br /> <br /> * Home page http://www.intermine.org/<br /> <br /> * About Intermine http://intermine.org/wiki/InterMine<br /> <br /> * Intermine Overview http://intermine.org/wiki/InterMineOverview<br /> <br /> * Prerequisite and downloading http://intermine.org/wiki/GettingStarted http://intermine.org/wiki/Prerequisites<br /> <br /> * Hardware requirements http://intermine.org/wiki/Hardware<br /> <br /> * QuickStart http://intermine.org/wiki/QuickStart<br /> <br /> * TroubleShooting http://intermine.org/wiki/TroubleshootingTips<br /> <br /> * Download/Get intermine http://intermine.org/wiki/SVNCheckout<br /> <br /> * Intermine use cases http://intermine.org/wiki/InterMineUseCases<br /> <br /> <br /> <br /> ==Examples of databases using Intermine ==<br /> <br /> * RatMine: http://ratmine.mcw.edu/<br /> * modENCODE: http://www.modencode.org/<br /> * Flymine: http://www.flymine.org/<br /> * Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do<br /> * Targetmine : http://targetmine.nibio.go.jp/<br /> * Metabolicmine : http://www.metabolicmine.org/<br /> <br /> == Installation notes for Intermine on Ubuntu 64bit==<br /> <br /> <br /> <br /> <br /> Step A: Install all prerequistite tools required for Intermine installation<br /> <br /> The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites<br /> <br /> '''Additional install notes''' . This Installation is done on a Virtual box (running on win 7 64bits).<br /> <br /> 1. Install subversion <br /> sudo apt-get install subversion<br /> <br /> 2. Install sunjava6jdk<br /> sudo add-apt-repository &quot;deb http://archive.canonical.com/ lucid partner&quot; (added a source repository)<br /> Or add following to the /etc/apt/osurcelist<br /> deb http://archive.canonical.com/ubuntu lucid partner<br /> deb-src http://archive.canonical.com/ubuntu lucid partner<br /> Commands to run - <br /> sudo apt-get update<br /> sudo apt-get install sun-java6-jdk<br /> <br /> 3. Install ant<br /> a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/<br /> b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26<br /> c. export ANT_HOME=/home/ranjit/ant (ant is in my home directory)<br /> d. export PATH=${PATH}:${ANT_HOME}/bin<br /> These variable can be included in a batch script which automatically runs after system login. <br /> <br /> 4. Install Tomcat <br /> Download tomcat, unzip it and place it at a location you know.<br /> Just start/stop the server as (ant is in my home directory)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) <br /> Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml ($CATALINA_HOME is the installation directory)<br /> &lt;tomcat-users&gt;<br /> &lt;!-- you can add more users or roles if needed --&gt;<br /> &lt;role rolename=&quot;manager&quot;/&gt;<br /> &lt;user username=&quot;manager&quot; password=&quot;manager&quot; roles=&quot;manager&quot;/&gt;<br /> &lt;/tomcat-users&gt;<br /> <br /> Add java memmory requirements<br /> To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR<br /> Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell: export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”<br /> If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.<br /> <br /> 5. Install postgresql 8.4<br /> sudo apt-get install postgresql-8.4<br /> Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites<br /> sudo vim /etc/postgresql/8.4/main/postgresql.conf<br /> Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)<br /> Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf to use &quot;md5&quot; MD5 authentication<br /> sudo /etc/init.d/postgresql-8.4 restart (restart the server)<br /> <br /> Install Bioseg into postgres<br /> sudo apt-get install postgresql-contrib-8.4<br /> sudo apt-get install postgresql-server-dev-8.4<br /> Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ <br /> Unzip and Install it as<br /> make USE_PGXS=t clean<br /> make USE_PGXS=t<br /> make USE_PGXS=t install<br /> <br /> When a database is created it can be added to it by<br /> psql (database) &lt;bioseg.sql<br /> psql (database) &lt;btree_gist.sql<br /> To start/stop/restart postgressql do..<br /> sudo /etc/init.d/postgresql-8.4 start (replace start with stop/restart)<br /> <br /> 6.Install Junit<br /> Download from http://www.junit.org/<br /> Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)<br /> Add to the java classpath with this command, replacing X.X with the version number.<br /> like<br /> export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar<br /> <br /> <br /> <br /> ----</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=Intermine&diff=3527 2012-01-07T22:47:00Z

<p>Rkumar@uab.edu: /* Web Resources for Intermine */</p> <hr /> <div>== Motivation ==<br /> <br /> CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service. <br /> <br /> <br /> == Web Resources for Intermine == <br /> <br /> * Home page http://www.intermine.org/<br /> <br /> * About Intermine http://intermine.org/wiki/InterMine<br /> <br /> * Intermine Overview http://intermine.org/wiki/InterMineOverview<br /> <br /> * Prerequisite and downloading http://intermine.org/wiki/GettingStarted http://intermine.org/wiki/Prerequisites<br /> <br /> * Hardware requirements http://intermine.org/wiki/Hardware<br /> <br /> * QuickStart http://intermine.org/wiki/QuickStart<br /> <br /> * TroubleShooting http://intermine.org/wiki/TroubleshootingTips<br /> <br /> * Download/Get intermine http://intermine.org/wiki/SVNCheckout<br /> <br /> * Intermine use cases http://intermine.org/wiki/InterMineUseCases<br /> <br /> <br /> <br /> ==Examples of Inermine databases (active)==<br /> <br /> * RatMine: http://ratmine.mcw.edu/<br /> * modENCODE: http://www.modencode.org/<br /> * Flymine: http://www.flymine.org/<br /> * Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do<br /> * Targetmine : http://targetmine.nibio.go.jp/<br /> * Metabolicmine : http://www.metabolicmine.org/<br /> <br /> == Installation notes for Intermine on Ubuntu 64bit==<br /> <br /> <br /> <br /> <br /> Step A: Install all prerequistite tools required for Intermine installation<br /> <br /> The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites<br /> <br /> '''Additional install notes''' . This Installation is done on a Virtual box (running on win 7 64bits).<br /> <br /> 1. Install subversion <br /> sudo apt-get install subversion<br /> <br /> 2. Install sunjava6jdk<br /> sudo add-apt-repository &quot;deb http://archive.canonical.com/ lucid partner&quot; (added a source repository)<br /> Or add following to the /etc/apt/osurcelist<br /> deb http://archive.canonical.com/ubuntu lucid partner<br /> deb-src http://archive.canonical.com/ubuntu lucid partner<br /> Commands to run - <br /> sudo apt-get update<br /> sudo apt-get install sun-java6-jdk<br /> <br /> 3. Install ant<br /> a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/<br /> b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26<br /> c. export ANT_HOME=/home/ranjit/ant (ant is in my home directory)<br /> d. export PATH=${PATH}:${ANT_HOME}/bin<br /> These variable can be included in a batch script which automatically runs after system login. <br /> <br /> 4. Install Tomcat <br /> Download tomcat, unzip it and place it at a location you know.<br /> Just start/stop the server as (ant is in my home directory)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) <br /> Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml ($CATALINA_HOME is the installation directory)<br /> &lt;tomcat-users&gt;<br /> &lt;!-- you can add more users or roles if needed --&gt;<br /> &lt;role rolename=&quot;manager&quot;/&gt;<br /> &lt;user username=&quot;manager&quot; password=&quot;manager&quot; roles=&quot;manager&quot;/&gt;<br /> &lt;/tomcat-users&gt;<br /> <br /> Add java memmory requirements<br /> To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR<br /> Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell: export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”<br /> If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.<br /> <br /> 5. Install postgresql 8.4<br /> sudo apt-get install postgresql-8.4<br /> Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites<br /> sudo vim /etc/postgresql/8.4/main/postgresql.conf<br /> Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)<br /> Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf to use &quot;md5&quot; MD5 authentication<br /> sudo /etc/init.d/postgresql-8.4 restart (restart the server)<br /> <br /> Install Bioseg into postgres<br /> sudo apt-get install postgresql-contrib-8.4<br /> sudo apt-get install postgresql-server-dev-8.4<br /> Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ <br /> Unzip and Install it as<br /> make USE_PGXS=t clean<br /> make USE_PGXS=t<br /> make USE_PGXS=t install<br /> <br /> When a database is created it can be added to it by<br /> psql (database) &lt;bioseg.sql<br /> psql (database) &lt;btree_gist.sql<br /> To start/stop/restart postgressql do..<br /> sudo /etc/init.d/postgresql-8.4 start (replace start with stop/restart)<br /> <br /> 6.Install Junit<br /> Download from http://www.junit.org/<br /> Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)<br /> Add to the java classpath with this command, replacing X.X with the version number.<br /> like<br /> export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar<br /> <br /> <br /> <br /> ----</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=Intermine&diff=3526 2012-01-07T22:45:06Z

<p>Rkumar@uab.edu: </p> <hr /> <div>== Motivation ==<br /> <br /> CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service. <br /> <br /> <br /> == Web Resources for Intermine == <br /> <br /> * Home page http://www.intermine.org/<br /> <br /> * About Intermine http://intermine.org/wiki/InterMine<br /> <br /> * Intermine Overview http://intermine.org/wiki/InterMineOverview<br /> <br /> * Prerequisite and downloading http://intermine.org/wiki/GettingStarted http://intermine.org/wiki/Prerequisites<br /> <br /> * Hardware requirements http://intermine.org/wiki/Hardware<br /> <br /> * QuickStart http://intermine.org/wiki/QuickStart<br /> <br /> * TroubleShooting http://intermine.org/wiki/TroubleshootingTips<br /> <br /> * Download/Get intermine http://intermine.org/wiki/SVNCheckout<br /> <br /> * Intermine use cases http://intermine.org/wiki/InterMineUseCases<br /> <br /> <br /> Examples of Inermine databases (active)<br /> * RatMine: http://ratmine.mcw.edu/<br /> * modENCODE: http://www.modencode.org/<br /> * Flymine: http://www.flymine.org/<br /> * Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do<br /> * Targetmine : http://targetmine.nibio.go.jp/<br /> * Metabolicmine : www.metabolicmine.org/<br /> <br /> <br /> <br /> <br /> == Installation notes for Intermine on Ubuntu 64bit==<br /> <br /> <br /> <br /> <br /> Step A: Install all prerequistite tools required for Intermine installation<br /> <br /> The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites<br /> <br /> '''Additional install notes''' . This Installation is done on a Virtual box (running on win 7 64bits).<br /> <br /> 1. Install subversion <br /> sudo apt-get install subversion<br /> <br /> 2. Install sunjava6jdk<br /> sudo add-apt-repository &quot;deb http://archive.canonical.com/ lucid partner&quot; (added a source repository)<br /> Or add following to the /etc/apt/osurcelist<br /> deb http://archive.canonical.com/ubuntu lucid partner<br /> deb-src http://archive.canonical.com/ubuntu lucid partner<br /> Commands to run - <br /> sudo apt-get update<br /> sudo apt-get install sun-java6-jdk<br /> <br /> 3. Install ant<br /> a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/<br /> b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26<br /> c. export ANT_HOME=/home/ranjit/ant (ant is in my home directory)<br /> d. export PATH=${PATH}:${ANT_HOME}/bin<br /> These variable can be included in a batch script which automatically runs after system login. <br /> <br /> 4. Install Tomcat <br /> Download tomcat, unzip it and place it at a location you know.<br /> Just start/stop the server as (ant is in my home directory)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) <br /> Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml ($CATALINA_HOME is the installation directory)<br /> &lt;tomcat-users&gt;<br /> &lt;!-- you can add more users or roles if needed --&gt;<br /> &lt;role rolename=&quot;manager&quot;/&gt;<br /> &lt;user username=&quot;manager&quot; password=&quot;manager&quot; roles=&quot;manager&quot;/&gt;<br /> &lt;/tomcat-users&gt;<br /> <br /> Add java memmory requirements<br /> To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR<br /> Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell: export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”<br /> If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.<br /> <br /> 5. Install postgresql 8.4<br /> sudo apt-get install postgresql-8.4<br /> Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites<br /> sudo vim /etc/postgresql/8.4/main/postgresql.conf<br /> Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)<br /> Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf to use &quot;md5&quot; MD5 authentication<br /> sudo /etc/init.d/postgresql-8.4 restart (restart the server)<br /> <br /> Install Bioseg into postgres<br /> sudo apt-get install postgresql-contrib-8.4<br /> sudo apt-get install postgresql-server-dev-8.4<br /> Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ <br /> Unzip and Install it as<br /> make USE_PGXS=t clean<br /> make USE_PGXS=t<br /> make USE_PGXS=t install<br /> <br /> When a database is created it can be added to it by<br /> psql (database) &lt;bioseg.sql<br /> psql (database) &lt;btree_gist.sql<br /> To start/stop/restart postgressql do..<br /> sudo /etc/init.d/postgresql-8.4 start (replace start with stop/restart)<br /> <br /> 6.Install Junit<br /> Download from http://www.junit.org/<br /> Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)<br /> Add to the java classpath with this command, replacing X.X with the version number.<br /> like<br /> export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar<br /> <br /> <br /> <br /> ----</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=Intermine&diff=3525 2012-01-07T22:42:14Z

<p>Rkumar@uab.edu: </p> <hr /> <div>== Motivation ==<br /> <br /> CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service. <br /> <br /> <br /> == Web Resources (Links) == <br /> <br /> * http://intermine.org/wiki/Hardware<br /> * http://intermine.org/wiki/Prerequisites<br /> * http://intermine.org/wiki/GettingStarted<br /> <br /> Main website www.intermine.org/<br /> <br /> About Intermine http://intermine.org/wiki/InterMine<br /> <br /> Intermine Overview http://intermine.org/wiki/InterMineOverview<br /> <br /> Prerequisite and downloading http://intermine.org/wiki/GettingStarted<br /> http://intermine.org/wiki/Prerequisites<br /> <br /> Hardware requirements http://intermine.org/wiki/Hardware<br /> <br /> QuickStart http://intermine.org/wiki/QuickStart<br /> <br /> TroubleShooting http://intermine.org/wiki/TroubleshootingTips<br /> <br /> Download/Get intermine http://intermine.org/wiki/SVNCheckout<br /> <br /> Intermine use cases http://intermine.org/wiki/InterMineUseCases<br /> <br /> <br /> Examples of Inermine databases (active)<br /> RatMine: http://ratmine.mcw.edu/<br /> modENCODE: http://www.modencode.org/<br /> Flymine: http://www.flymine.org/<br /> Yeastmine : http://yeastmine.yeastgenome.org/yeastmine/begin.do<br /> Targetmine : http://targetmine.nibio.go.jp/<br /> Metabolicmine : www.metabolicmine.org/<br /> <br /> <br /> <br /> <br /> == Installation notes for Intermine on Ubuntu 64bit==<br /> <br /> <br /> <br /> <br /> Step A: Install all prerequistite tools required for Intermine installation<br /> <br /> The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites<br /> <br /> '''Additional install notes''' . This Installation is done on a Virtual box (running on win 7 64bits).<br /> <br /> 1. Install subversion <br /> sudo apt-get install subversion<br /> <br /> 2. Install sunjava6jdk<br /> sudo add-apt-repository &quot;deb http://archive.canonical.com/ lucid partner&quot; (added a source repository)<br /> Or add following to the /etc/apt/osurcelist<br /> deb http://archive.canonical.com/ubuntu lucid partner<br /> deb-src http://archive.canonical.com/ubuntu lucid partner<br /> Commands to run - <br /> sudo apt-get update<br /> sudo apt-get install sun-java6-jdk<br /> <br /> 3. Install ant<br /> a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/<br /> b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26<br /> c. export ANT_HOME=/home/ranjit/ant (ant is in my home directory)<br /> d. export PATH=${PATH}:${ANT_HOME}/bin<br /> These variable can be included in a batch script which automatically runs after system login. <br /> <br /> 4. Install Tomcat <br /> Download tomcat, unzip it and place it at a location you know.<br /> Just start/stop the server as (ant is in my home directory)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) <br /> Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml ($CATALINA_HOME is the installation directory)<br /> &lt;tomcat-users&gt;<br /> &lt;!-- you can add more users or roles if needed --&gt;<br /> &lt;role rolename=&quot;manager&quot;/&gt;<br /> &lt;user username=&quot;manager&quot; password=&quot;manager&quot; roles=&quot;manager&quot;/&gt;<br /> &lt;/tomcat-users&gt;<br /> <br /> Add java memmory requirements<br /> To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR<br /> Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell: export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”<br /> If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.<br /> <br /> 5. Install postgresql 8.4<br /> sudo apt-get install postgresql-8.4<br /> Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites<br /> sudo vim /etc/postgresql/8.4/main/postgresql.conf<br /> Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)<br /> Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf to use &quot;md5&quot; MD5 authentication<br /> sudo /etc/init.d/postgresql-8.4 restart (restart the server)<br /> <br /> Install Bioseg into postgres<br /> sudo apt-get install postgresql-contrib-8.4<br /> sudo apt-get install postgresql-server-dev-8.4<br /> Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ <br /> Unzip and Install it as<br /> make USE_PGXS=t clean<br /> make USE_PGXS=t<br /> make USE_PGXS=t install<br /> <br /> When a database is created it can be added to it by<br /> psql (database) &lt;bioseg.sql<br /> psql (database) &lt;btree_gist.sql<br /> To start/stop/restart postgressql do..<br /> sudo /etc/init.d/postgresql-8.4 start (replace start with stop/restart)<br /> <br /> 6.Install Junit<br /> Download from http://www.junit.org/<br /> Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)<br /> Add to the java classpath with this command, replacing X.X with the version number.<br /> like<br /> export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar<br /> <br /> <br /> <br /> ----</div>

Rkumar@uab.edu https://docs.uabgrid.uab.edu/w/index.php?title=Intermine&diff=3524 2012-01-07T22:38:31Z

<p>Rkumar@uab.edu: </p> <hr /> <div>== Motivation ==<br /> <br /> CCTS/BMI group plans to establish an Intermine server at UAB in order to support genomics (and other -omic) reseach. The tool provides a way to link datasets with disparate datatypes together in a single warehouse. We particularly expect it to be useful for the analysis of gene sets: storage, collaboration/sharing and researcher self-service. <br /> <br /> <br /> == Web Resources (Links) == <br /> <br /> * http://intermine.org/wiki/Hardware<br /> * http://intermine.org/wiki/Prerequisites<br /> * http://intermine.org/wiki/GettingStarted<br /> <br /> <br /> <br /> == Installation notes for Intermine on Ubuntu 64bit==<br /> <br /> <br /> <br /> <br /> Step A: Install all prerequistite tools required for Intermine installation<br /> <br /> The basic notes for Installation are present on the Intermine website at http://intermine.org/wiki/Prerequisites<br /> <br /> '''Additional install notes''' . This Installation is done on a Virtual box (running on win 7 64bits).<br /> <br /> 1. Install subversion <br /> sudo apt-get install subversion<br /> <br /> 2. Install sunjava6jdk<br /> sudo add-apt-repository &quot;deb http://archive.canonical.com/ lucid partner&quot; (added a source repository)<br /> Or add following to the /etc/apt/osurcelist<br /> deb http://archive.canonical.com/ubuntu lucid partner<br /> deb-src http://archive.canonical.com/ubuntu lucid partner<br /> Commands to run - <br /> sudo apt-get update<br /> sudo apt-get install sun-java6-jdk<br /> <br /> 3. Install ant<br /> a. Download ant from http://www.reverse.net/pub/apache//ant/binaries/apache-ant-1.8.2-bin.tar.gz or http://ant.apache.org/<br /> b. export JAVA_HOME=/usr/lib/jvm/java-6-sun-1.6.0.26<br /> c. export ANT_HOME=/home/ranjit/ant (ant is in my home directory)<br /> d. export PATH=${PATH}:${ANT_HOME}/bin<br /> These variable can be included in a batch script which automatically runs after system login. <br /> <br /> 4. Install Tomcat <br /> Download tomcat, unzip it and place it at a location you know.<br /> Just start/stop the server as (ant is in my home directory)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/startup.sh (to start the server)<br /> /home/ranjit/apache-tomcat-6.0.33/bin/shutdown.sh (to stop it) <br /> Add a manager for tomcat by editing file $CATALINA_HOME/conf/tomcat-users.xml ($CATALINA_HOME is the installation directory)<br /> &lt;tomcat-users&gt;<br /> &lt;!-- you can add more users or roles if needed --&gt;<br /> &lt;role rolename=&quot;manager&quot;/&gt;<br /> &lt;user username=&quot;manager&quot; password=&quot;manager&quot; roles=&quot;manager&quot;/&gt;<br /> &lt;/tomcat-users&gt;<br /> <br /> Add java memmory requirements<br /> To avoid java.lang.OutOfMemory errors, specify the JVM heap size in $TOMCAT_HOME/bin/tomcat.sh. You can specify '-Xmx256m -Xms128m' as part of TOMCAT_OPTS. OR<br /> Edit the file $TOMCAT_HOME/bin/startup.sh and insert the following line, substituting for the desired value, eg. Bash Shell: export CATALINA_OPTS=”-Xms(min heap)m -Xmx(max heap)m”<br /> If you get the error message: java.lang.OutOfMemoryError: PermGen space you need to add the argument -XX:MaxPermSize=128m to CATALINA_OPTS, in addition to any argument you use to set the heap size.<br /> <br /> 5. Install postgresql 8.4<br /> sudo apt-get install postgresql-8.4<br /> Make following changes in file as suggested in postgre installation section of intermine page at http://intermine.org/wiki/Prerequisites<br /> sudo vim /etc/postgresql/8.4/main/postgresql.conf<br /> Create/Identify a userid and password. (help https://help.ubuntu.com/8.04/serverguide/C/postgresql.html)<br /> Edit sudo vim /etc/postgresql/8.4/main/pg_hba.conf to use &quot;md5&quot; MD5 authentication<br /> sudo /etc/init.d/postgresql-8.4 restart (restart the server)<br /> <br /> Install Bioseg into postgres<br /> sudo apt-get install postgresql-contrib-8.4<br /> sudo apt-get install postgresql-server-dev-8.4<br /> Download bioseg from http://www.bioinformatics.org/bioseg/wiki/ <br /> Unzip and Install it as<br /> make USE_PGXS=t clean<br /> make USE_PGXS=t<br /> make USE_PGXS=t install<br /> <br /> When a database is created it can be added to it by<br /> psql (database) &lt;bioseg.sql<br /> psql (database) &lt;btree_gist.sql<br /> To start/stop/restart postgressql do..<br /> sudo /etc/init.d/postgresql-8.4 start (replace start with stop/restart)<br /> <br /> 6.Install Junit<br /> Download from http://www.junit.org/<br /> Copy to the ant lib directory, (may be apache-ant-1.6.5/lib/)<br /> Add to the java classpath with this command, replacing X.X with the version number.<br /> like<br /> export CLASSPATH=/home/ranjit/ant/lib/junit4.10/junit-4.10.jar<br /> <br /> <br /> <br /> ----</div>

Rkumar@uab.edu