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INSTALL.md

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Installation Instructions

Installing SageMath 9

The cgt package requires a version of SageMath that is based on Python 3 (as opposed to Python 2). If you're used to Python 2, the only thing that will need changing in your existing code will be print statements (they will need to be changed from print x to print(x)).

Follow the instructions located here. Ignore the package manager solutions, the version of SageMath you will get from those is very outdated, at least on Ubuntu.

The basic steps (for Linux) are:

  • Download binaries. You will most likely need the 64bit version. Choose the latest one for your operating system, making sure the OS version is the same.
  • Make a directory on your machine called Sage or similar, where you will place the sage installation. Move the file you downloaded into this folder.
  • Extract the files using tar. For example: tar -xjf sage-9.3-Ubuntu_20.04-x86_64.tar.bz2 After extracting, you can delete the .bz2 file.
  • cd into SageMath and run sage for the first time by executing the sage file. Wait for it to finish loading, to the point where you get the sage prompt and can type commands. Exit sage.
  • Run the command sudo ln -s /path/to/SageMath/sage /usr/local/bin/sage You can now start SageMath from any directory by typing sage.

Installing Circular Genome Tools

After completing the above steps, execute the command sage -pip install cgt. When you import the package, it will warn you of any missing python packages you might need to install, inclding scipy, matplotlib and networkx.