Installing QIIME manually in it's own prefix on CentOS 6.5. Our cluster has a network-mounted applications directory, so I wanted to install it once there, so all cluster nodes could use it.
- Reference: http://qiime.org/install/install.html
QIIME wants this specific version, so let's compile and install it into the qiime/1.8.0 prefix.
Prepare Python source:
$ cd /tmp
$ wget https://www.python.org/ftp/python/2.7.3/Python-2.7.3.tar.xz
$ tar xf Python-2.7.3.tar.xz
$ cd Python-2.7.3
Use newer GCC if available:
$ scl enable devtoolset-2 bash
Configure and build:
$ ./configure --prefix=/export/apps/qiime/1.8.0
$ sudo mkdir -p /export/apps/qiime/1.8.0
$ sudo chown aorth:aorth /export/apps/qiime/1.8.0
$ make install
$ curl https://bootstrap.pypa.io/get-pip.py | /export/apps/qiime/1.8.0/bin/python
Install QIIME and dependencies using the python from above:
$ export PATH=/export/apps/qiime/1.8.0/bin:$PATH
QIIME wants NumPy:
$ pip install numpy==1.7.1
QIIME wants MatPlotLib:
$ cd /tmp
$ wget -c 'http://downloads.sourceforge.net/project/matplotlib/matplotlib/matplotlib-1.3.1/matplotlib-1.3.1.tar.gz?r=&ts=1404890842&use_mirror=garr' -O matplotlib-1.3.1.tar.gz
$ tar zxf matplotlib-1.3.1.tar.gz
$ cd matplotlib-1.3.1
$ python setup.py build
$ python setup.py install
QIIME wants PyCogent:
$ pip install cogent==1.5.3
QIIME wants biom-format:
$ pip install biom-format==1.3.1
QIIME wants qcli:
$ pip install qcli==0.1.0
QIIME wants pynast:
$ pip install pynast==1.2.2
QIIME wants Emperor:
$ pip install emperor==0.9.3
QIIME itself:
$ cd /tmp
$ wget https://pypi.python.org/packages/source/q/qiime/qiime-1.8.0.tar.gz
$ tar xf qiime-1.8.0.tar.gz
$ cd qiime-1.8.0
$ export PATH=/export/apps/qiime/1.8.0/bin:$PATH
$ scl enable devtoolset-2 bash
$ sudo mkdir -p /export/apps/qiime/1.8.0
$ sudo chown aorth:aorth /export/apps/qiime/1.8.0
$ python setup.py install --install-scripts=/export/apps/qiime/1.8.0/bin --install-purelib=/export/apps/qiime/1.8.0/lib
Set up the config:
$ cp /export/apps/qiime/1.8.0/lib/qiime/support_files/qiime_config /export/apps/qiime/1.8.0/qiime_config
$ export QIIME_CONFIG_FP=/export/apps/qiime/1.8.0/qiime_config
Test QIIME:
$ export PYTHONPATH=/export/apps/qiime/1.8.0/lib:$PYTHONPATH
$ print_qiime_config.py -t
Dependencies for a "full" QIIME... install them into qiime/1.8.0 prefix:
Infernal 1.0.2:
$ cd /tmp
$ wget ftp://selab.janelia.org/pub/software/infernal/infernal-1.0.2.tar.gz
$ cd infernal
$ cd infernal-1.0.2
$ ./configure --prefix=/export/apps/qiime/1.8.0
$ make
$ make install
R 3.0.2:
$ cd /tmp
$ wget http://cran.r-project.org/src/base/R-3/R-3.0.2.tar.gz
$ tar xf R-3.0.2.tar.gz
$ cd R-3.0.2
$ ./configure --enable-R-shlib --prefix=/export/apps/qiime/1.8.0
$ make -j4
$ make install
Install R modules by running the following R script, libraries.R:
options(repos="http://cran.case.edu")
install.packages('randomForest')
install.packages('optparse')
install.packages('vegan')
install.packages('ape')
install.packages('MASS')
install.packages('gtools')
install.packages('klaR')
install.packages('RColorBrewer')
q()
$ /export/apps/qiime/1.8.0/bin/R CMD BATCH libraries.R
Mothur 1.25.0:
$ cd /tmp
$ wget http://www.mothur.org/w/images/6/6d/Mothur.1.25.0.zip
$ unzip Mothur.1.25.0.zip
$ cd Mothur.source
$ sed -i 's/#CXX = g++44/CXX = g++/' makefile
$ sed -i 's/TARGET_ARCH += -arch x86_64/#TARGET_ARCH += -arch x86_64/' makefile
$ sed -i 's/#CXXFLAGS += -mtune=native -march=native -m64/CXXFLAGS += -mtune=native -march=native -m64/' makefile
$ sed -i 's/$LINK_OPTS//' uchime_src/mk
$ make
$ cp mothur uchime /export/apps/qiime/1.8.0/bin
Legacy NCBI BLAST 2.2.22:
$ cd /tmp
$ wget http://mirrors.vbi.vt.edu/mirrors/ftp.ncbi.nih.gov/blast/executables/release/2.2.22/blast-2.2.22-x64-linux.tar.gz
$ tar xf blast-2.2.22-x64-linux.tar.gz
$ cp blast-2.2.22/bin/* /export/apps/qiime/1.8.0/bin
tax2tree 1.0:
$ wget 'http://downloads.sourceforge.net/project/tax2tree/tax2tree-v1.0.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Ftax2tree%2Ffiles%2Ftax2tree-v1.0.tar.gz%2Fdownload%3Fuse_mirror%3Dtene&ts=1415126866&use_mirror=tenet' -O tax2tree-v1.0.tar.gz
$ tar xf tax2tree-v1.0.tar.gz
$ cd tax2tree-v1.0
$ python setup.py build
$ python setup.py install
$ wget http://drive5.com/cgi-bin/upload3.py?license=2014110411231511736 -O usearch
$ sudo cp usearch /export/apps/qiime/1.8.0/bin
$ sudo chmod +x /export/apps/qiime/1.8.0/bin/usearch
$ wget http://drive5.com/cgi-bin/upload3.py?license=2014110411322525582 -O usearch61
$ sudo cp usearch61 /export/apps/qiime/1.8.0/bin
$ sudo chmod +x /export/apps/qiime/1.8.0/bin/usearch61
rtax 0.984:
$ wget http://static.davidsoergel.com/rtax-0.984.tgz
$ tar xf rtax-0.984.tgz
$ sudo mkdir -p /export/apps/rtax
$ sudo cp -r rtax-0.984 /export/apps/rtax/0.984
$ sudo chown -R root:root /export/apps/rtax/0.984
SourceTracker 0.9.5:
$ cd /tmp
$ wget 'http://downloads.sourceforge.net/project/sourcetracker/sourcetracker-0.9.5.tar.gz?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fsourcetracker%2Ffiles%2Fsourcetracker-0.9.5.tar.gz%2Fdownload%3Fuse_mirror%3Dheanet&ts=1415266680&use_mirror=heanet' -O sourcetracker-0.9.5.tar.gz
$ tar xf sourcetracker-0.9.5.tar.gz
$ sudo mkdir /export/apps/sourcetracker
$ sudo cp -r sourcetracker-0.9.5 /export/apps/sourcetracker/0.9.5
$ sudo chown -R root:root /export/apps/sourcetracker/0.9.5
ClearCut v1.0.9:
$ cd /tmp
$ wget http://www.mothur.org/w/images/9/91/Clearcut.source.zip
$ unzip Clearcut.source.zip
$ cd clearcut
$ scl enable devtoolset-2 bash
$ make
$ sudo cp clearcut /export/apps/qiime/1.8.0/bin
Test!
$ print_qiime_config.py -t
Change permissions back to root!
$ sudo chown -R root:root /export/apps/qiime/1.8.0