|# save this file somewhere on your disk. open your terminal, and go there. then type these commands:|
|# chmod +x anvi-ubuntu-setup.sh|
|# and then get some coffee, and come back to see whether it's your lucky day.|
|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|
|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|
|tar -zxvf v2.6.2.tar.gz && cd Prodigal-2.6.2/ && make|
|sudo cp prodigal /usr/bin/|
|rm -rf v2.6.2.tar.gz Prodigal-2.6.2|
|tar -zxvf hmmer-3.1b2.tar.gz|
|sudo make install|
|rm -rf hmmer-3.1b2 hmmer-3.1b2.tar.gz|
|# install anvio|
|sudo pip install anvio|
Apr 6, 2016
Hey @JohnYu-yuzhongyi, thank you very much for your interest! I corrected the URL.
Jul 7, 2016
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'
Nov 15, 2018
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.
Oct 28, 2022
I am facing problem while installing anvio's in unbuntu 18.04 setup. should I make some changes in python version in the install python-pip line. I already have python3 in the system. With this code in bash script "sudo pip install -r final-reqs.txt", the download is not proceeding beyond line 10 of "final-reqs.txt" but as I changed to pip3 it proceeded to line 17 and then again the error states that
"Collecting pandas>=1.2.1 (from -r final-reqs.txt (line 18))
Could not find a version that satisfies the requirement pandas>=1.2.1 (from -r final-reqs.txt (line 18)) (from versions: 0.1, 0.2, 0.3.0, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.5.0, 0.6.0, 0.6.1, 0.7.0, 0.7.1, 0.7.2, 0.7.3, 0.8.0, 0.8.1, 0.9.0, 0.9.1, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.13.0, 0.13.1, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.15.2, 0.16.0, 0.16.1, 0.16.2, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 0.19.2, 0.20.0, 0.20.1, 0.20.2, 0.20.3, 0.21.0, 0.21.1, 0.22.0, 0.23.0, 0.23.1, 0.23.2, 0.23.3, 0.23.4, 0.24.0, 0.24.1, 0.24.2, 0.25.0, 0.25.1, 0.25.2, 0.25.3, 1.0.0, 1.0.1, 1.0.2, 1.0.3, 1.0.4, 1.0.5, 1.1.0, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5)
No matching distribution found for pandas>=1.2.1 (from -r final-reqs.txt (line 18))"
Could you please help me with a solution?
Also I am trying to install this package in server and another statement is shown to me while running this bash script.
"The directory '/home/adminuser/.cache/pip/http' or its parent directory is not owned by the current user and the cache has been disabled. Please check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag.
The directory '/home/adminuser/.cache/pip' or its parent directory is not owned by the current user and caching wheels has been disabled. check the permissions and owner of that directory. If executing pip with sudo, you may want sudo's -H flag."
Oct 28, 2022
This is quite dates now. You should follow the default installation instructions at anvio.org, @sowptika.
Nov 1, 2022
Thank you for the help.
Thanks for this! But the website of getting hmmer has been changed to eddylab.org, you might want to change it in the script.