Software for analyzing glycomics and glycoproteomics LC-MS/MS data

This package provides several command line tools, available under the name glycresoft.

$ glycresoft -h
Commands:
  analyze           Identify structures in preprocessed data
  build-hypothesis  Build search spaces for glycans and glycopeptides
  config            Set persistent configuration options
  export            Write Data Collections To Text Files
  mzml              Inspect and preprocess mzML files
  tools             Odds and ends to help inspect data and diagnose issues

This program requires Python 3.8 or newer. The simplest way to perform the installation is to use a virtual environment to isolate its dependencies. To install from source after cloning this repository:

make install-dependencies

This will install this library and all of its dependencies into the current Python environment. The command line tool will be made available under the name glycresoft.

If you want to build the standalone executable that bundles all of its dependencies with its own version of Python, next run

pip install PyInstaller
make build-pyinstaller

This will install PyInstaller, a Python program which can package another Python program and all of its dependencies into a native executable, and run it on an entry point wrapper for GlycReSoft. Afterwards, the standalone executable and its static files are located in ./pyinstaller/dist/glycresoft-cli/, where the executable is named glycresoft-cli, which will operate essentially the same as the glycresoft executable installed above, save that it will do some platform specific configuration and can be used from outside the virtual environment it was created in.