From aff2e78128a4097c3a5b63772189db805758b062 Mon Sep 17 00:00:00 2001
From: Timothy Divoll <timothy.divoll@gmail.com>
Date: Thu, 30 Nov 2023 12:18:05 -0500
Subject: [PATCH] docs: remove old readme content and reference new pipeline
 repo

---
 README.md | 38 ++++----------------------------------
 1 file changed, 4 insertions(+), 34 deletions(-)

diff --git a/README.md b/README.md
index e22b6a29..2bc5e9b3 100644
--- a/README.md
+++ b/README.md
@@ -9,6 +9,7 @@ Track Ice Floes using Moderate Resolution Imaging Spectroradiometer (MODIS) data
 ## Documentation 
 
 See the package's documentation (in development) at https://wilhelmuslab.github.io/IceFloeTracker.jl/
+
 ## Prerequisites
 
 A `julia` installation; ensure it is available on the `PATH`.
@@ -31,7 +32,7 @@ julia> ]
 ... to enter package mode.
 
 ```
-(@v1.7) pkg> activate IceFloeTracker.jl/
+(@v1.9) pkg> activate IceFloeTracker.jl/
 Activating project at `~/IceFloeTracker.jl`
 ```
 
@@ -41,7 +42,6 @@ Instantiate the environment and run the tests:
 (IceFloeTracker) pkg> test
 ```
 
-
 ## Notebooks
 
 To use notebooks with `IceFloeTracker.jl` you must activate the notebooks project and start Pluto
@@ -69,39 +69,9 @@ import IceFloeTracker
 
 You now have access to `IceFloeTracker` from inside your Pluto notebook!
 
-## Fetch Data
-
-The [`fetchdata.sh`](/scripts/fetchdata.sh) script requires the utilities [`gdal`](https://gdal.org/) and [`proj`](https://proj.org/). This repository includes a brewfile for ease of installation on MacOS. To install `gdal` and `proj` via homebrew, first [install homebrew](https://brew.sh/), then run `brew bundle install`
+## Using in a Pipeline
 
-### Example
-
-```
-$ ./scripts/fetchdata.sh -o data -s 2022-05-01 81 -22 79 -12
-```
-
-## Commandline
-
-To call each step of Ice Floe Tracker pipeline from the command line you can run:
-
-```
-./scripts/ice-floe-tracker.jl
-```
-
-Each step of the pipeline is implemented as a command to the script. Most commands take a metadata file, input directory, and output directory.
-
-For example:
-
-```
-./scripts/ice-floe-tracker.jl landmask <METADATA FILE> <INPUT DIR> <OUTPUT DIR>
-```
-
-## Snakemake
-
-Snakemake is used to encode the entire pipeline from start to finish. Snakemake relies on the command line scripts to automate the pipeline. The snakemake file should be suitable for runs on HPC systems. To run snakemake locally, run the following from a terminal in the root of this project:
-
-```
-snakemake -c<NUM CORES>
-```
+See the related tools at `https://github.com/WilhelmusLab/ice-floe-tracker-pipeline.git` for a Julia Command-line Interface to access all the source functions and templates for using the Cylc pipeline orchestrator.
 
 ## Development