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quinlan-lab / pathoscore

pathoscore evaluates variant pathogenicity tools and scores.
MIT License
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new gene sets and efficiency fixes to old gene formulae #62

Closed jimhavrilla closed 6 years ago

brentp commented 6 years ago

did you mean to commit the actual cancer gene list? we usually only include the recipe.

jimhavrilla commented 6 years ago

Yeah that one is custom

On Wed, Sep 12, 2018, 8:05 AM Brent Pedersen notifications@github.com wrote:

did you mean to commit the actual cancer gene list? we usually only include the recipe.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/62#issuecomment-420660667, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BJvF-UxkoLg4mAwWQacW0fARfySZks5uaRSWgaJpZM4Wk1Px .

jimhavrilla commented 6 years ago

I can put it on s3 if you prefer

On Wed, Sep 12, 2018, 9:03 AM Jim Havrilla semjaavria@gmail.com wrote:

Yeah that one is custom

On Wed, Sep 12, 2018, 8:05 AM Brent Pedersen notifications@github.com wrote:

did you mean to commit the actual cancer gene list? we usually only include the recipe.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/quinlan-lab/pathoscore/pull/62#issuecomment-420660667, or mute the thread https://github.com/notifications/unsubscribe-auth/AGQ8BJvF-UxkoLg4mAwWQacW0fARfySZks5uaRSWgaJpZM4Wk1Px .

jimhavrilla commented 6 years ago

Hey @brentp other than moving the gene set list to s3, is the PR good?

brentp commented 6 years ago

your call. I really don't understand what this is for or why the changes to grep.

jimhavrilla commented 6 years ago

Thanks.

We wanted some example gene sets to prerun for clinicians. It took a while to find some high quality ones. The grep fix is because for some reason the old formulae only work on Linux not MacOS UNIX. Weirdly enough.

On Wed, Sep 12, 2018, 7:41 PM Brent Pedersen notifications@github.com wrote:

your call. I really don't understand what this is for or why the changes to grep.

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