ANNOTATION: Hard-coded annotation paths & more

UCSF-Costello-Lab / LG3_Pipeline

The original LG3 pipeline

https://github.com/UCSF-Costello-Lab/LG3_Pipeline

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ANNOTATION: Hard-coded annotation paths & more #31

Closed HenrikBengtsson closed 3 years ago

HenrikBengtsson commented 6 years ago

Going to use this thread to scribble down when I discover other hardcoded paths to reference files but also to scripts (as the below example also includes):


$ head -10 FilterMutations/mutationConfig.cfg
[General]
genomeBuild = hg19

[AnnoVarInputs]
executable = /home/jocostello/shared/LG3_Pipeline/AnnoVar/annotate_variation.pl
dbDir = /home/jocostello/shared/LG3_Pipeline/AnnoVar/hg19db/
snpDBs = snp132
1kgDBs = 1000g2010nov_all,1000g2011may_all

[SNPRemovalFilters]

HenrikBengtsson commented 3 years ago

Moved to https://github.com/UCSF-Costello-Lab/LG3_Pipeline/issues/158#issuecomment-940399365