How to set up a new GEO project
You can use geofetch to quickly set up a project to run with looper.
Download data
geofetch -i GSE69993 --just-metadata -m metadata
Initialize looper
Make it easier to run looper without specifying the config
looper init metadata/*.yaml
Convert to fastq
Now, you can convert the files from sra into fastq format:
looper run --amend sra_convert
Run pipeline
Add a pipeline interface to link to a project
(Experimental)
looper mod "pipeline_interfaces: /path/to/piface.yaml"