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katerinakazantseva / strainy

Graph-based assembly phasing
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Flye as submodule #29

Closed mikolmogorov closed 1 year ago

mikolmogorov commented 1 year ago

Flye should be linked as a github submodule (see https://github.com/KolmogorovLab/hapdup as an example). Afterwards, instead of invoking flye through subprocess, we can import is as a Python package and invoke polisher without creating additional processes. This should make the installation and debugging easier + may help to speed up the entire pipeline a bit.

See the example how polisher is invoked here: https://github.com/fenderglass/Flye/blob/3f0ef0a6bd6710c97214ab465035413ce82d624e/flye/main.py#L502

mikolmogorov commented 1 year ago

Since currently Flye would't run as a Python package, for now run it in a separate Python interpreter (via subprocess). Path to Flye is currently hardcoded - but it should be changed to relative paths to submodule.

Once done, please update the metaPhase installation instructions accordingly.