Installation

You can install Trycycler using pip, either from a local copy:

git clone https://github.com/rrwick/Trycycler.git
pip3 install ./Trycycler
trycycler --help

Or directly from GitHub:

pip3 install git+https://github.com/rrwick/Trycycler.git
trycycler --help

Note that this will only install Trycycler itself and the Python packages it needs (Edlib, NumPy and SciPy). It will not install the external tools that Trycycler requires. For those, please look at the Software requirements page.

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

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, read on.

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 3.6).

Your installation command would then look like this:

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

GCC issues

Trycycler requires the Edlib package, which will be installed by pip when you install Trycycler. This process involves compiling C++ code, so your computer will need to have GCC or an equivalent compiler. If you are seeing an error like error: command 'gcc' failed with exit status 1, then read on.

Installing GCC on Linux

If you are using Ubuntu (or a related distribution), then you can use the apt package manager to get things set up:

sudo apt install build-essential

If you are using CentOS (or a related distribution), then this command should do the trick:

sudo yum groupinstall "Development Tools"

Installing GCC on MacOS

If you are using a Mac, then the standard way to get your compiler up and running is to install Xcode and its command line tools. This should give you a working gcc command.