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NCI-CGR / plco-analysis

Primary workflow for the PLCO "Atlas" project
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Makefile.config extension handling assumes python=3 #15

Closed lightning-auriga closed 3 years ago

lightning-auriga commented 3 years ago

which is bad, when ldsc/ldscores pipelines assume python2

lightning-auriga commented 3 years ago

this isn't actually much of a problem. the extensions are not required for ldscores pipelines, as far as I can tell. the simplest thing will be to wrap the extensions definitions in some test for /usr/bin/env python3 or whatever. the only impact right now is a bunch of ugly error messages that actually don't do anything, so... I could also just leave it, if it's too much of a pain for some reason.

lightning-auriga commented 3 years ago

I have successfully suppressed these spurious notifications with a test for python3 presence in the environment. There's a variety of other weird warnings that pop up if the wrong environment is loaded; but these were if the correct environment was loaded, which is unacceptable.