PhyloAcc is a mix of Python and C++ code with dependencies for each. As such, we do not support building from source as dependency
installation will vary from system to system. Instead, we offer a pre-built package through
bioconda which allows installation with the
This section outlines in detail the steps starting from installation of Anaconda to installation of PhyloAcc. If you already have
experience with Anaconda or
conda feel free to skip steps that you are familiar with.
While we don't have a dedicated build for Windows up on bioconda yet, you can still install and run on your Windows PC via the Windows Subsystem for Linux. This essentially installs a Linux distribution within Windows so that you can install Linux progams and run Linux commands, and it works pretty seamlessly.
Check here for more info on installing WSL. And once you do you should be able to activate a bash shell within your Windows Powershell and follow the instructions below for Linux.
1. Installing Anaconda
Anaconda is a distribution of the Python programming language with other software to facilitate data science tasks. We are
interested in the package manager associated with Anaconda,
conda, as it will handle the installation
of PhyloAcc and its dependencies. So, to use
conda we need to first install the Anaconda distribution.
If you are on an institutional server or cluster, it is possible they already have Anaconda and
installed and activated. You can check this by simply running the command:
If you see the text
conda X.XX.X, with each X being a number indicating the version, then
is already installed and you can skip to step 3!
To install Anacaonda, first navigate to the Anaconda downloads page and click on the link to download the install file.
The Anaconda website automatically detects the operating system of the computer that has browsed to the site and recommends the Anaconda version for that OS. If you are installing Anaconda on your personal computer this should be fine. However, if you are installing on a remote server or cluster the OS is likely different. Click on the appropriate version for the OS on your desired install system under Get Additional Installers to get the correct version.
This should download a
.sh file for Linux and OSX.
Next, place the downloaded file in the location on your system where you want
to install Anaconda. If you are installing on a remote server, you'll to need either download on that system directly with something like
wget or use another file transfer program to move the file over. You'll need to place this file somewhere on the
remote system where you have permission to run programs, like your home directory.
Finally, run the install script by running the command:
<filename> is the name of the script. Follow the prompts and let the script run and Anaconda should be installed!
2. Activating Anaconda
When Anaconda has been installed, it needs to be activated for the system to know to use its software (like
To activate, run:
/<path>/<to>/ is the location where you installed Anaconda. For instance, if you installed Anaconda
in your home directory, you should see the
anaconda3/ folder there, and you could activate with the command:
Once activated, you should be able to run
This should print out the text
conda X.XX.X, with each X being a number indicating the version. If you get an error at this point,
something has gone wrong with installation or activation and you'll need to re-visit those steps.
You may want Anaconda to be activated automatically when you login, you could add the
source /<path>/<to>/anaconda3/bin/activate command to your user profile. Your user
profile is located in your home directory, though it is hidden (use
ls -a to see hidden files). It will usually be called something like
.profile. If none of those files exist, you may be able to create them.
Open your profile file and add the command and save. It will then be run whenever you login. For more information about bash profiles
see: Bash startup files
3. Creating a conda environment for PhyloAcc
conda is able to install and solve package dependencies by working in environments, self-contained file systems
where the current user has full permissions. To create a new enviornment, run:
conda create -n <environment name>
<environment name> is something descriptive for the purpose of the environment. For instance, for installing and running
PhyloAcc, I would call this one
conda create -n phyloacc-env
Follow the prompts on the screen to create the environment.
4. Activating your PhyloAcc conda environment
Even though an envrionment has been created, to install software or run software you've already installed in it you must activate it:
conda activate phyloacc-env
You might notice that your command prompt changes based on which environment you have activated. If you ever wish to exit an environment,
5. Installing PhyloAcc from bioconda
Now that a Anaconda has been installed and a conda environment set up you are ready to install PhyloAcc from bioconda!
If this is your first time using conda or bioconda, you may have to set-up your channels. A channel is a remote host for different types of software. For instance, lots of biology related software is found in the bioconda channel and a lot of other software is found in the conda-forge channel. Since we are primarily interested in biological software, we want to make sure that bioconda has priority. Follow the instructions in the link above to setup channels for bioconda for the first time.
You can also change your channel order at any time by editing their order in your
in your home directory
To install PhyloAcc, run the command:
conda install phyloacc
Follow the prompts on the screen and wait for the dependencies to install. Once finished, you should be ready to run PhyloAcc! To make sure, run the command:
which should print out the version info for PhyloAcc and:
which ensures that the C++ binaries are installed. If you get an error during either of these commands, or one of the dependency checks fails, you will have to troubleshoot the installation process.
1. conda: command not found
If you see the
conda: command not found error when trying to install PhyloAcc it likely means:
- Anaconda isn't installed - See here for installation instructions
- Anaconda isn't activated - See here for activation instructions
2. conda cannot solve the environment
conda install phyloacc command fails or hangs for a long time the program might be struggling
with installing dependencies given the current settings. To solve this, try the following:
Make sure conda is up to date. To update conda, run the command:
conda update -n base -c defaults conda
- Make sure your channels are set-up to give bioconda priority
3. phyloacc.py: command not found
If you see the
phyloacc.py: command not found error some time after you have successfully run the
conda install phyloacc command, it likely means you aren't in the same environment as where you installed PhyloAcc. Make sure
you activate the correct conda environment.