Updated docs to refer to gene-oracle repo

Author: bentsherman

README.md

@@ -3,7 +3,7 @@
 This repository provides tools and instructions for running nextflow pipelines on a Kubernetes cluster. These scripts have been tested for the following pipelines:
 
 - [SystemsGenetics/GEMmaker](https://github.com/SystemsGenetics/GEMmaker)
-- [SystemsGenetics/gene-oracle-nf](https://github.com/SystemsGenetics/gene-oracle-nf)
+- [SystemsGenetics/gene-oracle](https://github.com/SystemsGenetics/gene-oracle)
 - [SystemsGenetics/KINC-nf](https://github.com/SystemsGenetics/KINC-nf)
 
 (In Progress) 

examples/gene-oracle.md

@@ -6,7 +6,7 @@ In this example you will use the [gene-oracle](https://github.com/SystemsGenetic
 
 We will use the `make-input-data.py` script in the gene-oracle repo to generate a "fake GEM" and a list of gene sets for that GEM. Clone the gene-oracle repo to your local machine, and then run the script:
 ```bash
-python <gene-oracle-path>/scripts/make-input-data.py --n-samples 1000 --n-genes 20 --n-sets 50
+python <gene-oracle-path>/bin/make-input-data.py --n-samples 1000 --n-genes 20 --n-sets 50
 ```
 
 It is recommended that you create a separate directory for each pipeline that you use, so that the data and nextflow metadata for each pipeline are separate:
@@ -42,7 +42,7 @@ Before running the pipeline, you must transfer your input data from your local m
 
 Then you can run the pipeline using nextflow's `kuberun` command:
 ```bash
-nextflow kuberun systemsgenetics/gene-oracle-nf -v <pvc-name>
+nextflow kuberun systemsgenetics/gene-oracle -v <pvc-name>
 ```
 
 ## Transfer Output Data