#!/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 | |
wget https://raw.githubusercontent.com/merenlab/anvio/master/requirements.txt -O all-reqs.txt | |
cat all-reqs.txt | grep -v numpy | grep -v scipy > final-reqs.txt | |
sudo pip install -r final-reqs.txt | |
# 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 |
Hey @JohnYu-yuzhongyi, thank you very much for your interest! I corrected the URL.
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'
Thans for this installer,
I had a failure with this script to install anvi'o v5.2 on ubuntu 16.4, since default pip is that of python 2 in the os. Instead of "pip", "pip3" seemed to be required for the package to be installed in L31 and L58.
Thanks for this! But the website of getting hmmer has been changed to eddylab.org, you might want to change it in the script.