make everything self contained, with no external dependencies on the Baker lab server

[Haddox]

@grocklin: I just wanted to give you a heads up that I am going to try to make a list of all external dependencies in the scoring pipeline and try to move them into the repo, or at least make a list of what they are and try to make it clear how to change the scripts so that they can be used by others not in the Baker lab. I imagine this might be useful to you in your new lab. The fragment-picking step is probably the biggest thing to take care of. Just wanted to let you know in case you've already though about how to set up fragment picking in your lab. Maybe there's an easy way where we could make the path to fragment-picking scripts an easily definable input variable to the scoring pipeline.

To do:

• np_aa_burial.py: line 14 calls rosetta_scripts

• make_fragments.py: relies on the Baker lab's fragment picker

[grocklin]

Pretty sure np_aa_burial is no longer necessarily, replaced by a filter

…

On Thu, Feb 14, 2019 at 9:46 AM Hugh Haddox ***@***.***> wrote: @grocklin <https://github.com/grocklin>: I just wanted to give you a heads up that I am going to try to make a list of all external dependencies in the scoring pipeline and try to move them into the repo, or at least make a list of what they are and try to make it clear how to change the scripts so that they can be used by others not on the Baker-lab. I imagine this might be useful to you in your new lab. The fragment-picking step is probably the biggest thing to take care of. Just wanted to let you know in case you've already though about how to set up fragment picking in your lab. Maybe there's an easy way where we could make the path to fragment-picking scripts an easily definable input variable to the scoring pipeline. To do: - np_aa_burial.py: line 14 calls rosetta_scripts - make_fragments.py: relies on the Baker lab's fragment picker — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AErvpwY1b8P0r2imI5egHW8DOAa36xTwks5vNaEPgaJpZM4a8HQ4> .

[Haddox]

Added a bunch of auxiliary scripts in commit 33ec237

[Haddox]

@grocklin: is it a filter that is already in the pipeline? Or do we need to add it? All the XMLs are in the directory scripts/xmls/ named according to the filter name.

[grocklin]

I think it's identical to buried_npsa_FAMILYVW

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On Thu, Feb 14, 2019 at 9:53 AM Hugh Haddox ***@***.***> wrote: @grocklin <https://github.com/grocklin>: is it a filter that is already in the pipeline? Or do we need to add it? All the XMLs are in the directory scripts/xmls/ named according to the filter name. — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#6 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AErvpyR8DLm_asUj6XtZwHH7UsjhtKYoks5vNaK0gaJpZM4a8HQ4> .