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INSTALLATION.md

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Install Whiscy

Below we will go into a step-by-step guide on how to install Whiscy. Instructions are provived for Ubuntu Linux, in other systems the installation process may vary.

Third-Party

Whiscy depends on the following third-party software:

  • Muscle
  • FreeSASA
  • HSSPCONV
  • Protdist

The installation of these dependencies is described in the THIRDPARTY.md file.

Whiscy

It can be easily installed from pip

pip install whiscy

Check the installation

$ whiscy -h
usage: whiscy [-h] [-o output_file] [--version]
              surface_list conversion_table alignment_file distance_file

positional arguments:
  surface_list          Surface list
  conversion_table      Conversion table
  alignment_file        Alignment file
  distance_file         Distance file

options:
  -h, --help            show this help message and exit
  -o output_file, --output output_file
                        If set, output prediction to this file
  --version             show program's version number and exit

Troubleshooting

If you get an error such as ValueError: MUSCLE_BIN not found in system variables, make sure you have followed the steps in THIRDPARTY.md to install the third-party dependencies.