Skip to content

Instantly share code, notes, and snippets.

@maasha

maasha/gist:4656341

Created January 28, 2013 15:21
Show Gist options

  • Select an option

    Learn more about clone URLs
  • Save maasha/4656341 to your computer and use it in GitHub Desktop.

Select an option

Learn more about clone URLs
Save maasha/4656341 to your computer and use it in GitHub Desktop.
Download ZIP
QIIME 1.6 Installation notes.
Raw
gistfile1.txt
QIIME-1.6.0 install
===================
Documentation: http://qiime.org/install/install.html
home = /home/maasha/
install = /home/maasha/install
prefix = /home/maasha/install/QIIME1.6/
source = /home/maasha/install/QIIME1.6/src/
bashrc = /home/maasha/install/QIIME1.6/bashrc
System
======
Linux orsted 3.2.0-0.bpo.1-amd64 #1 SMP Sat Feb 11 08:41:32 UTC 2012 x86_64 GNU/Linux
Debian 6.0.6
Prerequisites
=============
Installing Python-2.7.3
-----------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://www.python.org/ftp/python/2.7.3/Python-2.7.3.tgz
3. tar -zxvf Python-2.7.3.tgz
4. ln -s Python-2.7.3 Python
5. cd Python/
6. ./configure --prefix=/home/maasha/install/QIIME1.6/
7. make
8. make install
Installing PyCogent-1.5.3
-------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://downloads.sourceforge.net/project/pycogent/PyCogent/1.5.3/PyCogent-1.5.3.tgz
3. tar -zxvf PyCogent-1.5.3.tgz
4. ln -s PyCogent-1.5.3 PyCogent
5. cd PyCogent/
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Installing Numpy-1.5.1
----------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://downloads.sourceforge.net/project/numpy/NumPy/1.5.1/numpy-1.5.1.tar.gz
3. tar -zxvf numpy-1.5.1.tar.gz
4. ln -s numpy-1.5.1 numpy
5. cd numpy/
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Installing biom-format-1.1.1
----------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget ftp://thebeast.colorado.edu/pub/biom-format-releases/biom-format-1.1.1.tar.gz
3. tar -zxvf biom-format-1.1.1.tar.gz
4. ln -s biom-format-1.1.1 biom-format
5. cd biom-format/
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Installing Extras
=================
Installing uclust
-----------------
1. cd /home/maasha/install/QIIME1.6/bin/
2. wget http://www.drive5.com/uclust/uclustq1.2.22_i86linux64
3. ln -s uclustq1.2.22_i86linux64 uclust
4. chmod 755 uclustq1.2.22_i86linux64
Installing PyNast-1.2
---------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget https://github.com/downloads/qiime/pynast/PyNAST-1.2.tar.gz
3. tar -zxvf PyNAST-1.2.tar.gz
4. ln -s PyNAST-1.2 PyNAST
5. cd PyNAST/
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Installing FastTree-2.1.3
-------------------------
1. mkdir /home/maasha/install/QIIME1.6/src/FastTree
2. cd /home/maasha/install/QIIME1.6/src/FastTree
3. wget http://www.microbesonline.org/fasttree/FastTree-2.1.3.c
4. gcc -Wall -O3 -finline-functions -funroll-loops -o FastTree -lm FastTree-2.1.3.c
5. cd /home/maasha/install/QIIME1.6/bin/
6. ln -s ../src/FastTree/FastTree FastTree
Installing jre1.6.0_05
----------------------
(skipped -> evil)
Installing rdp_classifier-2.2
-------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://downloads.sourceforge.net/project/rdp-classifier/rdp-classifier/rdp_classifier_2.2.zip
3. unzip rdp_classifier_2.2.zip
4. add export RDP_JAR_PATH="$QIIMEPATH/src/rdp_classifier_2.2/rdp_classifier-2.2.jar" to bashrc
Installing usearch-5.2.32
-------------------------
1. obtain license: http://www.drive5.com/usearch/nonprofit_form.html
2. download binary to /home/maasha/install/QIIME1.6/bin/
3. chmod 755 usearch5.2.32_i86linux32
4. ln -s usearch5.2.32_i86linux32 usearch
Installing tax2tree 1.0.0
-------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget https://downloads.sourceforge.net/project/tax2tree/tax2tree-v1.0.tar.gz
3. tar -zxvf tax2tree-v1.0.tar.gz
4. ln -s tax2tree-v1.0 tax2tree
5. cd tax2tree/
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Installing blast-2.2.22
-----------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/release/2.2.22/blast-2.2.22-x64-linux.tar.gz
3. tar -zxvf blast-2.2.22-x64-linux.tar.gz
4. ln -s blast-2.2.22 blast
5. cd /home/maasha/install/QIIME1.6/bin/
6. for i in ../src/blast/bin/*; do ln -s $i `basename $i`; done
Installing CD-HIT-3.1.1
-----------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://www.bioinformatics.org/download/cd-hit/cd-hit-2007-0131.tar.gz
3. tar -zxvf cd-hit-2007-0131.tar.gz
4. cd cd-hit/
5. make
6. cd /home/maasha/install/QIIME1.6/bin
7. for i in cd-hit cd-hit-est cd-hit-2d cd-hit-est-2d cd-hit-div; do ln -s ../src/cd-hit/$i $i; done
Installing ChimeraSlayer
------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://downloads.sourceforge.net/project/microbiomeutil/microbiomeutil-r20110519.tgz
3. tar -zxvf microbiomeutil-r20110519.tgz
4. add export PATH="$QIIMEPATH/src/microbiomeutil-r20110519/ChimeraSlayer:$PATH" to bashrc
Installing Mothur-1.25.0
------------------------
1. mkdir /home/maasha/install/QIIME1.6/src/Mothur-1.25.0
2. cd /home/maasha/install/QIIME1.6/src/
3. ln -s Mothur-1.25.0 Mothur
4. cd Mothur/
5. wget http://www.mothur.org/w/images/6/6d/Mothur.1.25.0.zip
6. unzip Mothur.1.25.0.zip
7. cd Mothur.source/
8. edit makefile and comment out line 31: #TARGET_ARCH += -arch x86_64
9. make
10. cd /home/maasha/install/QIIME1.6/bin/
11. ln -s ../src/Mothur/Mothur.source/mothur mothur
Installing clearcut-1.0.9
-------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://www.mothur.org/w/images/9/91/Clearcut.source.zip
3. unzip Clearcut.source.zip
4. cd clearcut/
5. make
6. cd /home/maasha/install/QIIME1.6/bin/
7. ln -s ../src/clearcut/clearcut clearcut
Installing raxml-7.3.0
----------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget ftp://thebeast.colorado.edu/pub/QIIME-v1.5.0-dependencies/stamatak-standard-RAxML-5_7_2012.tgz
3. tar -zxvf stamatak-standard-RAxML-5_7_2012.tgz
4. ln -s stamatak-standard-RAxML-5_7_2012 raxml
5. cd raxml/
6. make -f Makefile.SSE3.gcc
7. cd /home/maasha/install/QIIME1.6/bin/
8. ln -s ../src/raxml/raxmlHPC-SSE3 raxmlHPC
Installing infernal-1.0.2
-------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget ftp://selab.janelia.org/pub/software/infernal/infernal.tar.gz
3. tar -zxvf infernal.tar.gz
4. ln -s infernal-1.0.2/ infernal
5. cd infernal/
6. ./configure --prefix=/home/maasha/install/QIIME1.6/
7. make
8. make install
Installing cdbtools
-------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/cdbfasta/cdbfasta.tar.gz
3. tar -zxvf cdbfasta.tar.gz
4. cd cdbfasta/
5. make
6. cd /home/maasha/install/QIIME1.6/bin/
7. ln -s ../src/cdbfasta/cdbfasta cdbfasta
8. ln -s ../src/cdbfasta/cdbyank cdbyank
Installing Muscle-3.8.31
------------------------
1. cd /home/maasha/install/QIIME1.6/bin/
2. wget http://www.drive5.com/muscle/downloads3.8.31/muscle3.8.31_i86linux64.tar.gz
3. tar -zxvf muscle3.8.31_i86linux64.tar.gz
4. ln -s muscle3.8.31_i86linux64 muscle
Installing rtax-0.983
----------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://static.davidsoergel.com/rtax-0.983.tgz
3. tar -zxvf rtax-0.983.tgz
4. ln -s rtax-0.983 rtax
5. cd /home/maasha/install/QIIME1.6/bin/
6. ln -s ../src/rtax/rtax rtax
Installing pplacer-1.1
----------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://matsen.fhcrc.org/pplacer/builds/pplacer-v1.1-Linux.tar.gz
3. tar -zxvf pplacer-v1.1-Linux.tar.gz
4. ln -s pplacer-v1.1.alpha13r2-Linux-2.6.32/ pplacer
5. cd /home/maasha/install/QIIME1.6/bin/
7. for i in guppy pplacer rppr; do ln -s ../src/pplacer/$i $i; done
Installing ParsInsert-1.04
--------------------------
1. mkdir /home/maasha/install/QIIME1.6/src/ParsInsert-1.04
2. cd /home/maasha/install/QIIME1.6/src/
3. ln -s ParsInsert-1.04 ParsInsert
4. cd ParsInsert/
5. wget http://downloads.sourceforge.net/project/parsinsert/ParsInsert.1.04.tgz
6. tar -zxvf ParsInsert.1.04.tgz
7. make
8. cd /home/maasha/install/QIIME1.6/bin/
9. ln -s ../src/ParsInsert/ParsInsert ParsInsert
Installing gsl-1.9
------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget ftp://ftp.gnu.org/gnu/gsl/gsl-1.9.tar.gz
3. tar -zxvf gsl-1.9.tar.gz
4. ln -s gsl-1.9 gsl
5. cd gsl/
6. ./configure --prefix=/home/maasha/install/QIIME1.6/
7. make
9. make install
Installing AmpliconNoiseV1.27
-----------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://ampliconnoise.googlecode.com/files/AmpliconNoiseV1.27.tar.gz
3. tar -zxvf AmpliconNoiseV1.27.tar.gz
4. ln -s AmpliconNoiseV1.27 AmpliconNoise
5. cd AmpliconNoise/
6. make
7. make install
8. cd /home/maasha/install/QIIME1.6/bin/
9. for i in ../src/AmpliconNoise/bin/*; do ln -s $i `basename $i`; done
Installing ghc-7.4.1
--------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://www.haskell.org/ghc/dist/7.4.1/ghc-7.4.1-src.tar.bz2
3. tar -jxvf ghc-7.4.1-src.tar.bz2
3. ln -s ghc-7.4.1 ghc
4. cd ghc/
6. ./configure --prefix=/home/maasha/install/QIIME1.6/
7. make
8. make install
Installing matplotlib-1.1.0
---------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://sourceforge.net/projects/matplotlib/files/matplotlib/matplotlib-1.1.0/matplotlib-1.1.0.tar.gz
3. tar -zxvf matplotlib-1.1.0.tar.gz
4. ln -s matplotlib-1.1.0 matplotlib
5. cd matplotlib/
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Installing cytoscape-2.8.3
--------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://chianti.ucsd.edu/Cyto-2_8_3/Cytoscape_2_8_3_unix.sh
3. sh Cytoscape_2_8_3_unix.sh
4. install in /home/maasha/install/QIIME1.6/
5. cd /home/maasha/install/QIIME1.6/bin/
6. ln -s ../Cytoscape_v2.8.3/cytoscape.sh cytoscape
Installing R-2.12
-----------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://mirrors.dotsrc.org/cran/src/base/R-2/R-2.12.0.tar.gz
3. tar -zxvf R-2.12.0.tar.gz
4. ln -s R-2.12.0 R
5. cd R/
6. ./configure --prefix=/home/maasha/install/QIIME1.6/
7. make
8. make install
9. ../../bin/R
10. install.packages('randomForest')
11. install.packages('optparse')
12. install.packages('vegan')
13. install.packages('ape')
14. install.packages('MASS') # not found?
15. install.packages('gtools')
16. install.packages('klaR')
17. install.packages('RColorBrewer')
18. q()
Installing Sphinx-1.1.3 (required to build html docs for Qiime)
---------------------------------------------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://pypi.python.org/packages/source/S/Sphinx/Sphinx-1.1.3.tar.gz
3. tar -zxvf Sphinx-1.1.3.tar.gz
4. ln -s Sphinx-1.1.3 Sphinx
5. cd Sphinx/
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Installing gdata-2.0.17 (use remove Google doc mapping files)
-------------------------------------------------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget http://gdata-python-client.googlecode.com/files/gdata-2.0.17.tar.gz
3. tar -zxvf gdata-2.0.17.tar.gz
4. ln -s gdata-2.0.17 gdata
5. cd gdata
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Installing tools from Roche
===========================
1. copy sfffile to /home/maasha/install/QIIME1.6/bin/
2. copy sffinfo to /home/maasha/install/QIIME1.6/bin/
Installing QIIME
================
Installing QIIME-1.6.0
----------------------
1. cd /home/maasha/install/QIIME1.6/src/
2. wget ftp://thebeast.colorado.edu/pub/qiime-releases/qiime-1.6.0.tar.gz
3. tar -xvf qiime-1.6.0.tar.gz
4. ln -s qiime-1.6.0 qiime
5. cd qiime/
6. ../../bin/python setup.py build
7. ../../bin/python setup.py install
Configuring QIIME1.6
--------------------
1. Users must add the following lines to their ~/.bashrc file:
if [ -f "$HOME/Install/QIIME1.6/bashrc" ]; then
/home/maasha/install/QIIME1.6/bashrc
fi
Then source .bashrc or relogin.
2. Users must copy configuration file to their home directory:
cp $QIIMEPATH/src/Qiime/qiime/support_files/qiime_config ~/.qiime_config
3. Test configuration by running
print_qiime_config.py -t
Installing data
===============
mkdir /home/maasha/install/QIIME1.6/data
Installling greengenes core set data file
-----------------------------------------
1. cd /home/maasha/install/QIIME1.6/data
2. wget http://greengenes.lbl.gov/Download/Sequence_Data/Fasta_data_files/core_set_aligned.fasta.imputed
3. edit ~/.qiime_config and set pynast_template_alignment_blastdb /home/maasha/install/QIIME1.6/data/core_set_aligned.fasta.imputed
Installing greengenes alignment lanemask file
---------------------------------------------
1. cd /home/maasha/install/QIIME1.6/data
2. wget http://greengenes.lbl.gov/Download/Sequence_Data/lanemask_in_1s_and_0s
3. edit ~/.qiime_config and set template_alignment_lanemask_fp /home/maasha/install/QIIME1.6/data/lanemask_in_1s_and_0s
Installing greengenes taxonomy
------------------------------
1. cd /home/maasha/install/QIIME1.6/data
2. wget ftp://greengenes.microbio.me/greengenes_release/gg_12_10/gg_12_10_otus.tar.gz
3. tar -zxvf gg_otus_4feb2011.tgz
3. edit ~/.qiime_config and set pynast_template_alignment_fp /home/maasha/install/QIIME1.6/data/gg_12_10_otus/rep_set/97_otus.fasta
The bashrc file (/home/maasha/install/QIIME1.6/bashrc)
===================================================
QIIMEPATH="/home/maasha/install/QIIME1.6"
export BLASTMAT="$QIIMEPATH/src/blast/data"
export PATH="$QIIMEPATH/bin:$PATH"
export PATH="$QIIMEPATH/src/microbiomeutil-r20110519/ChimeraSlayer:$PATH"
export PATH="$QIIMEPATH/src/AmpliconNoise/Scripts:$PATH"
export PATH="$QIIMEPATH/src/AmpliconNoise/bin:$PATH"
export PYTHONPATH="$QIIMEPATH/src/PyCogent:$PYTHONPATH"
export PYTHONPATH="$QIIMEPATH/lib:$PYTHONPATH"
export RDP_JAR_PATH="$QIIMEPATH/src/rdp_classifier_2.2/rdp_classifier-2.2.jar"
export PYRO_LOOKUP_FILE="$QIIMEPATH/src/AmpliconNoise/Data/LookUp_E123.dat"
export SEQ_LOOKUP_FILE="$QIIMEPATH/src/AmpliconNoise/Data/Tran.dat"
The .qiime_config file (~/.qiime_config)
========================================
# qiime_config
# WARNING: DO NOT EDIT OR DELETE Qiime/qiime_config
# To overwrite defaults, copy this file to $HOME/.qiime_config or a full path
# specified by $QIIME_CONFIG_FP and edit that copy of the file.
cluster_jobs_fp /home/maasha/Install/QIIME/bin/start_parallel_jobs.py
python_exe_fp python
working_dir
blastmat_dir /home/maasha/install/QIIME/src/blast/data
blastall_fp blastall
pynast_template_alignment_fp /home/maasha/install/QIIME1.6/data/gg_12_10_otus/rep_set/97_otus.fasta
pynast_template_alignment_blastdb /home/maasha/install/QIIME/data/core_set_aligned.fasta.imputed
template_alignment_lanemask_fp /home/maasha/install/QIIME/data/lanemask_in_1s_and_0s
jobs_to_start 10
seconds_to_sleep 60
qiime_scripts_dir /home/maasha/Install/QIIME/bin
temp_dir /tmp
denoiser_min_per_core 50
cloud_environment False
topiaryexplorer_project_dir
torque_queue friendlyq
Martin's comments
=================
1. I did not install Java. I fear building Java from source, so relying on Debian packages.
2. Fix for denoiser where the FlowgramAli_4frame binary for some reason is mislocated:
cp /home/maasha/install/QIIME1.6/src/Qiime-1.6.0/qiime/support_files/denoiser/bin/FlowgramAli_4frame
/home/maasha/install/QIIME1.6/lib/python2.7/site-packages/qiime/support_files/denoiser
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment