- Painless installation with Conda
- Installation (with varying levels of pain)
- Running the “Mini Test”
The latest version of anvi’o is
v5.5. See the release notes.
This article explains basic steps of installing anvi’o using rather conventional methods.
Please consider opening an issue for technical problems, or join us on Slack if you need help:
A note on Chrome
Currently, the Chrome Web Browser has the most efficient SVG engine among all browsers we tested. For instance, Safari can run the anvi’o interactive interface, however it takes orders of magnitude more time and memory compared to Chrome. Firefox, on the other hand, doesn’t even bother drawing anything at all. Long story short, the anvi’o interactive interface will not perform optimally with anything but Chrome. So you need Chrome. Moreover, if Chrome is not your default browser, every time interactive interface pops up, you will need to copy-paste the address bar into a Chrome window. You can learn what is your default browser by running this command in your terminal:
python -c 'import webbrowser as w; w.open_new("http://")'
Painless installation with Conda
This is a very simple and effective way to install anvi’o on your system along with all of its dependencies (we thank John Eppley for pushing us towards this direction). For this to work, you need miniconda to be installed on your system. If you are not sure whether it is installed or not, open a terminal (hopefully an iTerm if you are using Mac) and type
conda. You should see an output like this instead of a ‘command not found’ error (your version might be different):
$ conda --version conda 4.6.2
If you don’t have conda installed, then you should first install it through their installation page. Once you have confirmed you have conda installed, you are golden.
Run this command to install the latest stable version of anvi’o:
conda install -n anvio5 -c bioconda -c conda-forge anvio=5.5.0
Note that the most up-to-date conda-available anvi’o version, which is currently
v5.5, may differ from the most up-to-date stable anvi’o version, which is
v5.5 according to our headquarters at Westeros.
If you get an
EnvironmentLocationNotFound error from the previous command, try what Bruno Gomez-Gil suggested instead:
conda create -n anvio5 -c bioconda -c conda-forge anvio=5.5.0
Note: One of our users who has been trying conda installation on an HPC system reported the following steps working for them:
conda create -y --name anvio5 python=3.6 conda install -y --name anvio5 -c bioconda -c conda-forge anvio=5.5.0
Once the installation is complete, test anvi’o quickly to make sure everything is in order:
anvi-self-test --suite mini
IMPORTANT NOTE: You may need to activate the anvi’o conda environment every time you open a new terminal window. Depending on your conda setup, you will either need to run
source activate anvio5 or
conda activate anvio5 (this assumes you named your conda environment for anvio
anvio5 as per the commands above using the
--name flag –if not, please replace
anvio5 with whatever you have used to name your environment).
Installation (with varying levels of pain)
First things first: nothing here is as scary as it looks, and you can do it.
Firs, you will need to make sure your system does have all the following software if you are going to follow any of the following installation instructions. If you just follow these links, you will most probably be golden:
Finally you will need
virtualenv. This should work for most:
pip install virtualenv
If you don’t have
pip, you will need to visit this web page to have it installed.
Please note, anvi’o uses Python 3 exclusively.
If you run into any trouble, send an e-mail to Google Groups for anvi’o.
OK. If made through the section above, you may have gone through the most painful part already, and anvi’o developers are very proud of you.
Installing the latest stable release (safe mode)
This is the best way to install the stable release (but not the best way if you would like to synchronize your anvi’o to the development version, for which you should jump to the ‘active codebase’ section).
You will do everything in a Python virtual environment. If you are not experienced with computer thingies, do not worry. If you have taken care of your dependencies mentioned above, the rest should be very simple.
We first need to create a new virtual environment for anvi’o. Since it is easier to keep all virtual environments in one place, I will first create a directory in my home:
Then we will create a new virtual environment for anvi’o under that directory, to activate it, and to check the Python version in it to make sure the version starts with
virtualenv ~/virtual-envs/anvio-5.5 source ~/virtual-envs/anvio-5.5/bin/activate python --version
If using venv, run
python3 -m venv ~/virtual-envs/anvio-5.5
If using conda, run
python3 -m virtualenv ~/virtual-envs/anvio-5.5
The output of the last command must start with
Python 3. If not, remove the virtual environment with
rm -rf ~/virtual-envs/anvio, and find out how can you create a virtual environment for Python 3 on your system. You can try
-p python3 as a parameter to your
virtualenv command. Or you can type
virtualenv and without pressing the space character press
TAB key twice quickly to see if there is an alternative binary such as
virtualenv-3.5. If not, it means Python 3 is not installed on your system.
Make sure your paths look alright. Yours should look similar to this:
(anvio-5.5) meren ~ $ which pip /Users/meren/virtual-envs/anvio-5.5/bin/pip
A note on Python 3.7
This box is only relevant to you if you are using Python version 3.7. In that case some dependencies will fail to install as their latest stable release is not compatible with this Python version. For these dependencies you need to install development versions.
pip install https://github.com/scikit-learn/scikit-learn/archive/4035e60a6f0a0a2546bf0442ab603961c6a9cc4a.zip
Datrie (Dependency of snakemake)
pip install https://github.com/ozcan/datrie/releases/download/0.7.1/datrie-0.7.1.tar.gz
Or from original source:
wget https://github.com/pytries/datrie/archive/0.7.1.tar.gz tar xf 0.7.1.tar.gz cd datrie-0.7.1 ./update_c.sh python3.7 setup.py build python3.7 setup.py install
After installing these dependencies you should be able to install anvi’o. But when you run
anvi-profile --version. The anvi’o version may show up as
vunknown. This happens when the version of an anvi’o depenceny does not match to what anvi’o expects. You can always check the actual version of anvi’o with
pip show anvio or
pip list | grep anvio.
Now you can do the installation:
pip install numpy pip install scipy pip install cython pip install anvio
If all looks good, now you should be able to run
anvi-self-test --suite mini
You may see warning messages during self-test runs. Don’t be concerned.
If this runs successfully, a browser window will popup. Don’t forget to go back to your terminal and press
CTRL+C to kill the server. To leave the virtual environment, you can run the command
Now every time you want to use anvi’o, you will need to activate the virtual environment. If you like things to be convenient as much as we do, you may want to run the following command so you have a new command,
anvi-activate that activates your anvi’o installation:
echo 'alias anvi-activate-v5.5="source ~/virtual-envs/anvio-5.5/bin/activate"' >> ~/.bash_profile
When I open a new terminal, things look like this:
meren ~ $ anvi-interactive -v -bash: anvi-interactive: command not found meren ~ $ anvi-activate-v5.5 (anvio) meren ~ $ anvi-interactive -v Anvi'o version ...............................: 5.5 Profile DB version ...........................: 20 Contigs DB version ...........................: 8 Pan DB version ...............................: 5 Samples information DB version ...............: 2 Genome data storage version ..................: 1 Auxiliary data storage version ...............: 3 Anvi'server users data storage version .......: 1 (anvio) meren ~ $
Installing or updating from the active codebase (because why not)
This will allow you to go beyond the stable version and follow the very current version of the codebase (we assume you already have taken of your dependencies).
Let’s setup a new virtual environment and activate it:
virtualenv ~/virtual-envs/anvio-dev source ~/virtual-envs/anvio-dev/bin/activate python --version
If using conda, run
python3 -m virtualenv ~/virtual-envs/anvio-dev
Don’t forget to make sure the output of the last command starts with
I need to get the codebase
So this is your first time with the codebase. Get a fresh copy (with all the submodules necessary):
cd git clone --recursive https://github.com/meren/anvio.git
Then go into the
anvio directory, and then run the installation:
cd anvio source ~/virtual-envs/anvio-dev/bin/activate pip install -r requirements.txt python setup.py install
I already have the codebase
So you want to update your already existing installation. Follow these steps:
Now it is time to run
anvi-self-test --suite mini, of course.
If you want to make things simpler, you can add an alias to your
~/.bash_profile to easily switch to this environment:
echo 'alias anvi-activate-dev="source ~/virtual-envs/anvio-dev/bin/activate"' >> ~/.bash_profile
Installation for developers (you’re a wizard, arry)
This is the best option to keep up-to-date with day-to-day updates from anvi’o developers.
If you are planning to do this, you really need no introductions, but I will give you one anyway. Clone the codebase into a
$DIR you like:
Create a virtual environment (
master to remind you that you are following the GitHub
master), and do the initial setup, and leave it:
If using conda, run
python3 -m virtualenv ~/virtual-envs/anvio-master instead of the line that starts wth
virtualenv down below.
virtualenv ~/virtual-envs/anvio-master source ~/virtual-envs/anvio-master/bin/activate python --version # make sure the output starts with `Python 3`. cd $DIR/anvio # don't forget to update the $DIR with the real path pip install -r requirements.txt python setup.py build cp build/lib.*/anvio/*so anvio/ rm -rf anvio.egg-info build dist deactivate
Then update your activation batch to add necessary environment variables:
Please note that you need to update the
$DIR variable to whichever directory you cloned the codebase on your system before running the following lines in your terminal.
echo 'export PYTHONPATH=$PYTHONPATH:$DIR/anvio/' >> ~/virtual-envs/anvio-master/bin/activate echo 'export PATH=$PATH:$DIR/anvio/bin:$DIR/anvio/sandbox' >> ~/virtual-envs/anvio-master/bin/activate
That’s it. If you like, add an alias to your
~/.bash_profile to activate this quickly:
echo 'alias anvi-activate-master="source ~/virtual-envs/anvio-master/bin/activate"' >> ~/.bash_profile source ~/.bash_profile
Finally, if you would like to pull the latest commits from GitHub every time you switch to the
master, add these to your activation batch (you will need to update
$DIR once again):
echo 'cd $DIR/anvio && git pull && cd -' >> ~/virtual-envs/anvio-master/bin/activate
You are golden.
Running the “Mini Test”
You can make anvi’o test itself by running the program
anvi-self-test. It is absolutely normal to see ‘warning’ messages. In most cases anvi’o is talkative, and would like to keep you informed. You should read those warning messages carefully, but they often don’t require any action.
Upon the successful completion of all the tests, your browser should popup and take you to the interactive interface. When you click that ‘Draw’ button whenever you see one. One of those interfaces should look something like this (this is one of the older version of the anvi’o interactive interface, and it shall stay here so we remember where we came from):
All fine? Perfect! Now you have a running installation of anvi’o!
It is time to go through some anvi’o tutorials (see the pull-down menu at the top of this page), or take a look at all the other posts on the platform.