diff --git a/docs/using-geofetch.md b/docs/using-geofetch.md new file mode 100644 index 000000000..113b1252d --- /dev/null +++ b/docs/using-geofetch.md @@ -0,0 +1,35 @@ +# How to set up a new GEO project + +You can use [geofetch](http://geofetch.databio.org) 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" +``` diff --git a/mkdocs.yml b/mkdocs.yml index 99d543814..660070ded 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -23,6 +23,7 @@ nav: - Running multiple pipelines: multiple-pipelines.md - Writing a pipeline interface: writing-a-pipeline-interface.md - Create looper config file: how_to_define_looper_config.md + - Using geofetch: using-geofetch.md - Using divvy: - Introduction: README_divvy.md - Install and configure: install_divvy.md