Create a gist now

Instantly share code, notes, and snippets.

What would you like to do?
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

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

Owner

meren commented Apr 6, 2016

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

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'

Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment