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brendanofallon / jovian

Detecting variants in NGS short read data by sequence-to-sequence modeling
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Installable #34

Closed Luobiny closed 2 years ago

brendanofallon commented 2 years ago

This looks great, thank you! I guess we will have to figure out what we want to do about that "ssw_aligner" repo - that still needs to be installed manually - but maybe there's some way we can refer to it in pip_requirements or something?

Luobiny commented 2 years ago

Can we install ssw_aligner by pip? I did put "ssw_aligner" in the pip_requirements.txt file. From the ssw_aligner web page, I noticed that we just need to install Numpy, Cython, and then ssw_aligner itself through pip. Numpy is already in pip_requirements.txt, maybe we just need to add "Cython" to it?