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Installation issues
In the Badread installation instructions, I used the pip3 command to ensure that the installation is done with Python 3 (as many systems will have both Python 2 and 3 installed). However, depending on how you've installed your copy of Python 3, you may not have pip3 and could get an error like Command 'pip3' not found. If this happens to you, read on.
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/Badread.git
If you don't have pip3 and you can't use pip (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/Badread.git
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/.
Badread requires the Edlib package, which will be installed by pip when you install Badread. 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.
If you are using Ubuntu (or a closely 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 closely related distribution), then this command should do the trick:
sudo yum groupinstall "Development Tools"
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.