Relocate spot-deconvolution files and code to this repo

[lcolladotor]

Same as #86 but for the spot deconvolution code. Since lots at spython was exploratory, I think here it'll mostly involve only relocating code and adapting it, rather than moving files over. That is, adding new subdirectories at code/, that will then lead to new output files at processed-data/.

However, I might be wrong and there might be some spython output files that we do want to move to this repo. If so, we'll need to use some of the same strategy as at #86 with checking ACLs and writing code at code/_jhpce_org for the mv / rsync commands.

[lcolladotor]

$ nfs4_getfacl /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC

# file: /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spatialDLPFC
A::OWNER@:rwaDxtTcCy
A::GROUP@:rwaDxtcy
A:g:lieber_lcolladotor@cm.cluster:rwaDxtcy
A:g:lieber_marmaypag@cm.cluster:rwaDxtcy
A:g:hickslab@cm.cluster:rwaDxtcy
A::EVERYONE@:tcy
A:fdi:OWNER@:rwaDxtTcCy
A:fdi:GROUP@:rwaDxtcy
A:fdig:lieber_lcolladotor@cm.cluster:rwaDxtcy
A:fdig:lieber_marmaypag@cm.cluster:rwaDxtcy
A:fdig:hickslab@cm.cluster:rwaDxtcy
A:fdi:EVERYONE@:tcy

$ nfs4_getfacl /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spython/

# file: /dcs04/lieber/lcolladotor/spatialDLPFC_LIBD4035/spython/
A::OWNER@:rwaDxtTcCy
A::GROUP@:rwaDxtcy
A:g:lieber_lcolladotor@cm.cluster:rwaDxtcy
A:g:lieber_marmaypag@cm.cluster:rwaDxtcy
A:g:hickslab@cm.cluster:rwaDxtcy
A::EVERYONE@:tcy
A:fdi:OWNER@:rwaDxtTcCy
A:fdi:GROUP@:rwaDxtcy
A:fdig:lieber_lcolladotor@cm.cluster:rwaDxtcy
A:fdig:lieber_marmaypag@cm.cluster:rwaDxtcy
A:fdig:hickslab@cm.cluster:rwaDxtcy
A:fdi:EVERYONE@:tcy

I think it's the same ACLs (double check though), so mv commands should work ^^

[lcolladotor]

Remember to document the mv code at code/_jhpce_org, thanks!

[Nick-Eagles]

This is complete for Tangram. I created new scripts in code based on ones in spython, but no file transfers were required from spython to spatialDLPFC. I'll leave this issue open for now in case I also work on relocating cell2location-related files.

[lcolladotor]

ok, sounds good Nick! Thanks for the update =)