Installation

Installing with conda

If you like using conda to manage your software, there is a Trycycler conda recipe you can use. This has the advantage of taking care of Trycycler's software requirements for you. Brief disclaimer: I didn't create that recipe myself nor am I very savvy with conda, so I make no guarantees!

Before you begin, you'll need to make sure that you have added both bioconda and conda-forge channels. Run conda config --show channels and ensure that these are on your list. If not, add them.

You can then create an environment for Trycycler:

conda create --name trycycler

Activate it:

conda activate trycycler

And install:

conda install trycycler

That's it! Just remember that you'll need to activate your environment (via conda activate trycycler) before running Trycycler.

Installing with pip

If you prefer to install/manage your software without conda, then you can install Trycycler via pip instead.

You can install Trycycler 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.

Local installation

If you are installing Trycycler 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 Trycycler.

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

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

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

To use Trycycler 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 Trycycler, 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 3.6).

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 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/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 see something 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 a compiler is to install Xcode and its command line tools. This should give you a working gcc command.

Out-of-date GCC

If when trying to compile Edlib, you see a message that looks like this:

/usr/include/Availability.h:503:18: error: missing binary operator before token "("
 #if __has_include(<AvailabilityProhibitedInternal.h>)

...then that probably means you are using an old version of GCC. The __has_include construct was added in GCC v5, so version 5 or later should work better!