Software requirements and installation

Software requirements

Verticall runs on macOS and Linux. It requires Python 3.7 or later. It also uses a few Python packages (NumPy, pandas, Matplotlib and plotnine) but these should be taken care of by the installation process.

Verticall also requires that you have minimap2 installed. To verify that you do, try running this command:

minimap2 --help

If you see its usage instructions printed to the terminal, it's installed!

Installing with pip

You can install Verticall from a local copy:

git clone https://github.com/rrwick/Verticall.git
pip3 install ./Verticall
verticall --help

Or directly from GitHub:

pip3 install git+https://github.com/rrwick/Verticall.git
verticall --help

Note that this will only install Verticall itself and the Python packages it needs (NumPy, pandas, Matplotlib and plotnine). It will not install minimap2 which Verticall requires (see above).

If one of the above commands works for you, then you're done! If not, read on.

Local installation

If you are installing Verticall on a system that isn't yours (e.g. a shared server), you might encounter a permission error when running pip. For example: Could not install packages due to an EnvironmentError: [Errno 13] Permission denied. In this case, you might want to consider having an administrator install it for you. This is a good option if other users of the system also need to use Verticall.

Alternatively, if you just want to install Verticall for yourself, you can add --user to the pip command:

pip3 install --user git+https://github.com/rrwick/Verticall.git

This will install Verticall in your home directory (probably ~/.local/) where special permissions are not required. More information here.

To use Verticall after a local install, your local binary directory (~/.local/bin) will need to be in your PATH variable. This is a handy thing to set up in general, not just for Verticall, so I'd recommend adding it if it's not already there. Check out this page for a more in-depth discussion.

Pip issues

Above, I used the pip3 command to ensure that the installation is done with Python 3 (as many systems will have both Python 2 and Python 3 installed). However, depending on how your copy of Python 3 is installed, you may not have pip3 and could get an error like Command 'pip3' not found. If this happens to you, try one of the following.

Use pip

It may be that you simply have to use pip instead of pip3. But do make sure that your pip is for Python 3 and not Python 2 by running pip --version. Its output should end with something like (python 3.7).

Your installation command would then look like this:

pip install git+https://github.com/rrwick/Verticall.git

Use python3 -m pip

If you don't have pip3 and you can't use pip (e.g. because your pip is for Python 2), then you can try using the slightly more verbose python3 -m pip instead.

Your installation command would then look like this:

python3 -m pip install git+https://github.com/rrwick/Verticall.git

Installing pip

If none of the above work for you, you probably don't have pip installed at all. Check out this page for instructions on installing it: pip.pypa.io/en/stable/installing.