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QIIME_from_Scratch.sh
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QIIME_from_Scratch.sh
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#!/bin/sh
echo Installing JAVA:
sudo apt -y install default-jdk
sudo apt -y install default-jre
echo Installing RStudio
sudo echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" | sudo tee -a /etc/apt/sources.list
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | sudo apt-key add -
sudo apt-get update
sudo apt-get -y install r-base r-base-dev
wget -c https://download1.rstudio.org/rstudio-xenial-1.1.456-amd64.deb
sudo dpkg -i rstudio-xenial-1.1.456-amd64.deb
rm rstudio-xenial-1.1.456-amd64.deb
sudo apt-get -f install
echo Installing via QIIME deploy packages
sudo apt-get -y install python-dev libncurses5-dev libssl-dev libzmq-dev libgsl0-dev libxml2 libxslt1.1 libxslt1-dev ant git subversion build-essential zlib1g-dev libpng12-dev libfreetype6-dev mpich libreadline-dev gfortran unzip ghc sqlite3 libsqlite3-dev libc6-i386 libbz2-dev tcl-dev tk-dev r-base r-base-dev libatlas-dev libatlas-base-dev liblapack-dev swig libhdf5-serial-dev
echo Installing numpy, h5py and upgrade pip
sudo apt-get -y install build-essential python-dev python-pip
sudo pip install --upgrade pip
sudo pip install numpy
sudo pip install h5py
echo Installing STAMP, QIIME and matplotlib through pip
sudo apt-get -y install libblas-dev liblapack-dev gfortran
sudo apt-get -y install freetype* python-pip python-dev python-numpy python-scipy python-matplotlib
sudo apt-get -y install python-qt4
sudo pip install STAMP
sudo pip install qiime
sudo pip install matplotlib==1.4.3 # This is the required version for QIIME to run.
sudo apt-get -y upgrade
echo Installing the QIIME deploy: FULL QIIME Version
mkdir $HOME/QIIME
cd $HOME/QIIME/
git clone git://github.com/qiime/qiime-deploy.git
git clone git://github.com/qiime/qiime-deploy-conf.git
cd qiime-deploy/
python qiime-deploy.py $HOME/QIIME/ -f $HOME/QIIME/qiime-deploy-conf/qiime-1.9.1/qiime.conf --force-remove-failed-dirs
source $HOME/.bashrc
cd $HOME/QIIME
rm qiime-deploy
rm qiime-deploy-conf
echo Instalando Complementos para QIIME:
echo SeqPrep
cd
cd $HOME/QIIME/
git clone https://github.com/jstjohn/SeqPrep
cd SeqPrep
make
sudo echo 'export PATH=$HOME/QIIME/SeqPrep:$PATH' >> $HOME/.bashrc
echo fastq-join
cd $HOME/QIIME/
git clone https://github.com/brwnj/fastq-join
cd fastq-join
make
sudo echo 'export PATH=/$HOME/QIIME/fastq-join/:$PATH' >> $HOME/.bashrc
echo PICRUSt:
cd $HOME/QIIME/
git clone git://github.com/picrust/picrust.git picrust
cd picrust/picrust/data/
wget -c http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/16S_13_5_precalculated.tab.gz
wget -c http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/ko_13_5_precalculated.tab.gz
wget -c http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/rfam_13_5_precalculated.tab.gz
wget -c http://kronos.pharmacology.dal.ca/public_files/picrust/picrust_precalculated_v1.1.1/13_5/ko_13_5_precalculated.tab.gz
cd $HOME/QIIME/picrust
sudo pip install .
echo Update and Clean the system:
sudo apt-get -y update
sudo apt-get -y upgrade
sudo apt-get -y dist-upgrade
sudo apt-get -f install
sudo apt-get -y autoremove
sudo apt-get autoclean
echo Manually install the USEARCH Binaries: move them to PATH.
sudo mv usearch* /usr/local/bin/
sudo chmod +x /usr/local/bin/usarch*
## Eliminating me:
# rm $HOME/QIIME_from_Scratch.sh
exit