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QIIME Installation (Metagenomic Note)
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cd ~/Downloads
mkdir qiime_build
cd qiime_build
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Install required packages:
sudo apt-get -y install ghc python-numpy python-matplotlib
wget https://pypi
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org/packages/source/c/cogent/cogent-1
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5
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tgz
cd cogent-1
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sudo python setup
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wget "https://pypi
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org/packages/source/b/biom-format/biom-format-1
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gz"
tar -xzvf biom-format-1
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gz
cd biom-format-1
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sudo python setup
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wget http://nz
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ubuntu
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deb
sudo dpkg -i pyqi_0
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0-2_all
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archive
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com/ubuntu/pool/universe/p/python-qcli/python-qcli_0
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01_amd64
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1
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deb
wget https://pypi
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org/packages/source/p/pynast/pynast-1
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gz
tar -xzvf pynast-1
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gz
cd pynast-1
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sudo python setup
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wget https://pypi
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org/packages/source/e/emperor/emperor-0
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gz
tar -xzvf emperor-0
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gz
cd emperor-0
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sudo python setup
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wget http://www
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com/uclust/uclustq1
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22_i86linux64
sudo cp uclustq1
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22_i86linux64 /usr/local/bin/uclust
sudo chmod a+x /usr/local/bin/uclust
wget http://www
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org/fasttree/FastTree-2
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1
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c -lm
gcc -DOPENMP -fopenmp -O3 -finline-functions -funroll-loops -Wall -o FastTreeMP FastTree2
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Download Qiime installation package (Can be predownloaded):
wget "https://pypi
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org/packages/source/q/qiime/qiime1
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gz#md5=55bca3624114e81d33a2c2382bfb5266"
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tar
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Descend into the unpacked directory:
cd qiime-1
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py install
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Check Qiime configurations:
print_qiime_config
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q
topiaryexplorer_project_dir:
None
pynast_template_alignment_fp: None
cluster_jobs_fp: None
pynast_template_alignment_blastdb:
None
assign_taxonomy_reference_seqs_fp:
None
torque_queue: friendlyq
template_alignment_lanemask_fp:
None
jobs_to_start: 1
cloud_environment:
False
qiime_scripts_dir: None
denoiser_min_per_core:
50
working_dir: None
python_exe_fp: python
temp_dir:
/tmp/
blastall_fp:
blastall
seconds_to_sleep:
2
assign_taxonomy_id_to_taxonomy_fp:
None
============================================================
b
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Run testing script:
python all_tests
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Clean-up
cd ~/Downloads
sudo rm -r qiime_build
RDP Tools Installation
======================================================================
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Update software sources:
sudo apt-get update
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Clone RDPTools directory from GitHub:
git clone https://github
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git
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Pull RDPTools submodules from GitHub:
git submodule init;
git submodule update;
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net/projects/rdp-classifier/
The jar file can be used with multiple platforms
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org/install/install
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bpo
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cd /home/bioit/install/QIIME/src/
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python
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tgz
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tgz
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cd Python/
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make
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cd /home/bioit/install/QIIME/src/
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sourceforge
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5
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tar
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tar -zxvf numpy-1
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gz
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cd numpy/
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py build
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py install
Installing PyCogent-1
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------------------------1
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wget http://downloads
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net/project/pycogent/PyCogent/1
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1/PyCogent-1
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1
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tar -zxvf PyCogent-1
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ln -s PyCogent-1
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1 PyCogent
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/bin/python setup
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/bin/python setup
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cd /home/bioit/install/QIIME/src/
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python
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6c11
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gz
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6c11
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gz
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6c11 setuptools
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/bin/python setup
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/bin/python setup
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cd /home/bioit/install/QIIME/src/
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python
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1
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tar
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tar -zxvf Sphinx-1
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gz
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1
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cd Sphinx/
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py build
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py install
Installing biom-format-0
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---------------------------1
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wget https://github
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tgz
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tgz
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cd biom-format/
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py build
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py install
Installing QIIME
================
Installing QIIME-1
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---------------------1
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wget http://downloads
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net/project/qiime/releases/Qiime-1
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gz
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5
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tar
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ln -s Qiime-1
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0 Qiime
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/bin/python setup
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/bin/python setup
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Users must add the following line to their ~/
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bashrc or relogin
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Users must copy configuration file to their home directory:
cp $QIIMEPATH/src/Qiime/qiime/support_files/qiime_config ~/
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Test configuration by running
print_qiime_config
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cd /home/bioit/install/QIIME/bin/
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drive5
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ln -s uclustq1
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22_i86linux64 uclust
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2
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--------------------1
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wget http://downloads
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net/project/pynast/PyNAST%20releases/PyNAST-1
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tgz
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ln -s PyNAST-1
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cd PyNAST/
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py build
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py install
Installing matplotlib-1
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--------------------------1
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wget http://sourceforge
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tar
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tar -zxvf matplotlib-1
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gz
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cd matplotlib/
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py build
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py install
Installing cytoscape-2
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wget http://chianti
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edu/Cyto-2_8_3/Cytoscape_2_8_3_unix
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sh Cytoscape_2_8_3_unix
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install in /home/bioit/install/QIIME/
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ln -s
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sh cytoscape
Installing R-2
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cd /home/bioit/install/QIIME/src/
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dotsrc
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tar
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tar -zxvf R-2
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gz
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cd R/
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make
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/bin/R
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packages('randomForest')
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mkdir /home/bioit/install/QIIME/src/FastTree
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wget http://www
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org/fasttree/FastTree-2
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gcc -Wall -O3 -finline-functions -funroll-loops -o FastTree -lm FastTree
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cd /home/bioit/install/QIIME/bin/
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/src/FastTree/FastTree FastTree
Installing RDP classifier
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wget http://downloads
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net/project/rdp-classifier/rdpclassifier/rdp_classifier_2
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zip
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add export RDP_JAR_PATH="$QIIMEPATH/src/rdp_classifier_2
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obtain license: http://www
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com/usearch/nonprofit_form
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download binary to /home/bioit/install/QIIME/bin/
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ln -s usearch5
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32_i86linux32 usearch
Installing blast-2
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wget ftp://ftp
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nlm
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gov/blast/executables/release/2
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22/blast-2
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22-x64-linux
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gz
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2
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tar
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ln -s blast-2
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22 blast
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for i in
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cd /home/bioit/install/QIIME/src/
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bioinformatics
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tar
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tar -zxvf cd-hit-2007-0131
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gz
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make
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for i in cd-hit cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div; do ln -s
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cd /home/bioit/install/QIIME/src/
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sourceforge
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tgz
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tgz
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mkdir /home/bioit/install/QIIME/src/Mothur-1
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ln -s Mothur-1
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0 Mothur
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wget http://www
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org/w/images/6/6d/Mothur
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zip
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1
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0
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edit makefile and comment out line 31: #TARGET_ARCH += -arch x86_64
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cd /home/bioit/install/QIIME/bin/
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/src/Mothur/Mothur
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0
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cd /home/bioit/install/QIIME/src/
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mothur
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source
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unzip Clearcut
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zip
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make
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ln -s
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cd /home/bioit/install/QIIME/src/
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colorado
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tgz
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tgz
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cd raxml/
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SSE3
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cd /home/bioit/install/QIIME/bin/
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/src/raxml/raxmlHPC-SSE3 raxmlHPC
Installing infernal-1
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wget ftp://selab
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org/pub/software/infernal/infernal
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gz
3
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tar
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ln -s infernal-1
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2/ infernal
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configure --prefix=/home/bioit/install/QIIME/
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make install
Installing cdbtools
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wget ftp://occams
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harvard
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tar
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tar -zxvf cdbfasta
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gz
4
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make
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ln -s
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ln -s
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cd /home/bioit/install/QIIME/bin/
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drive5
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tar
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tar -zxvf muscle3
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31_i86linux64
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gz
4
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8
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981
---------------------1
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wget http://dev
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com/trac/rtax/raw-attachment/wiki/Releases/rtax-0
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tgz
3
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981
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ln -s rtax-0
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cd /home/bioit/install/QIIME/bin/
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/src/rtax/rtax rtax
Installing pplacer-1
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cd /home/bioit/install/QIIME/src/
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fhcrc
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1-Linux
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gz
3
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1-Linux
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gz
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1
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6
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cd /home/bioit/install/QIIME/bin/
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/src/pplacer/$i $i; done
Installing ParsInsert-1
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mkdir /home/bioit/install/QIIME/src/ParsInsert-1
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cd /home/bioit/install/QIIME/src/
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04 ParsInsert
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wget http://downloads
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net/project/parsinsert/ParsInsert
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04
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make
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ln -s
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----------------------------1
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wget http://ampliconnoise
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com/files/AmpliconNoiseV1
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tar
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tar -zxvf AmpliconNoiseV1
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tar
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ln -s AmpliconNoiseV1
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cd AmpliconNoise/
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make install
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for i in
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copy sfffile to /home/bioit/install/QIIME/bin/
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cd /home/bioit/install/QIIME/data
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lbl
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fasta
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edit ~/
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fasta
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cd /home/bioit/install/QIIME/data
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lbl
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edit ~/
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cd /home/bioit/install/QIIME/data
2
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lbl
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tgz
3
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tgz
3
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qiime_config and set pynast_template_alignment_fp
/home/bioit/install/QIIME/data/gg_otus_4feb2011/rep_set/gg_97_otus_4feb2011_aligned
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2/rdp_classifier-2
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jar"
export PYRO_LOOKUP_FILE="$QIIMEPATH/src/AmpliconNoise/Data/LookUp_E123
...
dat"
The
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qiime_config)
========================================
# qiime_config
# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config
# To overwrite defaults, copy this file to $HOME/
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cluster_jobs_fp /home/bioit/Install/QIIME/bin/start_parallel_jobs
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fasta
pynast_template_alignment_blastdb
/home/bioit/install/QIIME/data/core_set_aligned
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imputed
template_alignment_lanemask_fp /home/bioit/install/QIIME/data/lanemask_in_1s_and_0s
jobs_to_start 10
seconds_to_sleep
60
qiime_scripts_dir
/home/bioit/Install/QIIME/bin
temp_dir
/tmp
denoiser_min_per_core 50
cloud_environment
False
topiaryexplorer_project_dir
torque_queue friendlyq
Martin's comments
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I fear building Java from source, so relying on Debian packages