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Install anvi'o with all its dependencies on an Ubuntu 14.04 & 16.04
#!/bin/bash
# save this file somewhere on your disk. open your terminal, and go there. then type these commands:
#
# chmod +x anvi-ubuntu-setup.sh
# ./anvi-ubuntu-setup.sh
#
# and then get some coffee, and come back to see whether it's your lucky day.
set -e
export DEBIAN_FRONTEND=noninteractive
sudo apt-get update
# stuff to install with apt-get
sudo apt-get -y install python-pip
sudo apt-get -y install python-numpy
sudo apt-get -y install cython
sudo apt-get -y install libgsl0-dev
sudo apt-get -y install libblas-dev
sudo apt-get -y install liblapacke
sudo apt-get -y install gfortran libopenblas-dev liblapack-dev
sudo apt-get -y install zlibc zlib1g-dev zlib1g
sudo apt-get -y install sqlite
sudo apt-get -y install libhdf5-serial-dev
# pip
sudo pip install 'bottle>=0.12.9'
sudo pip install 'ete2>=2.3.10'
sudo pip install 'scikit-learn>=0.17.1'
sudo pip install 'django>=1.9.7'
sudo pip install 'h5py>=2.5.0'
sudo pip install 'scipy>=0.17.1'
sudo pip install 'cherrypy>=6.0.2'
sudo pip install 'requests>=2.10.0'
# prodigal
wget https://github.com/hyattpd/Prodigal/archive/v2.6.2.tar.gz
tar -zxvf v2.6.2.tar.gz && cd Prodigal-2.6.2/ && make
sudo cp prodigal /usr/bin/
cd
rm -rf v2.6.2.tar.gz Prodigal-2.6.2
# hmmer
wget http://eddylab.org/software/hmmer3/3.1b2/hmmer-3.1b2.tar.gz
tar -zxvf hmmer-3.1b2.tar.gz
cd hmmer-3.1b2
./configure
make
sudo make install
cd
rm -rf hmmer-3.1b2 hmmer-3.1b2.tar.gz
# install anvio
sudo pip install anvio
@JohnYu-yuzhongyi

Thanks for this! But the website of getting hmmer has been changed to eddylab.org, you might want to change it in the script.

@meren
Owner
meren commented Apr 6, 2016

Hey @JohnYu-yuzhongyi, thank you very much for your interest! I corrected the URL.

@bstamps
bstamps commented Jul 7, 2016 edited

Thanks for this! The order of the pip installs might need to be moved around though...

sudo pip install 'bottle>=0.12.9' sudo pip install 'ete2>=2.3.10' sudo pip install 'scikit-learn>=0.17.1' sudo pip install 'django>=1.9.7' sudo pip install 'h5py>=2.5.0' sudo pip install 'scipy>=0.17.1' sudo pip install 'cherrypy>=6.0.2' sudo pip install 'requests>=2.10.0'

I had a failure with the script on a base install of 14.04 with the above, but moving scipy above scikit-learn seems to have helped (As below).

sudo pip install 'bottle>=0.12.9' sudo pip install 'ete2>=2.3.10' sudo pip install 'scipy>=0.17.1' sudo pip install 'scikit-learn>=0.17.1' sudo pip install 'django>=1.9.7' sudo pip install 'h5py>=2.5.0' sudo pip install 'cherrypy>=6.0.2' sudo pip install 'requests>=2.10.0'

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