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Install anvi'o with all its dependencies on an Ubuntu 14.04 & 16.04
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#!/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 |
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Dear Meren,
Thank you for the help.
Best Wishes,
Sowptika