From 28eb6d8ae4689d1e9d596956e6612d0325f923f9 Mon Sep 17 00:00:00 2001
From: Ali Khan <alik@robarts.ca>
Date: Tue, 13 Feb 2024 09:26:36 -0500
Subject: [PATCH] update readme

---
 README.md | 30 +++++++++++++++++++++++++++++-
 1 file changed, 29 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index 23aa98d..a5c3194 100644
--- a/README.md
+++ b/README.md
@@ -5,9 +5,37 @@
 
 A Snakemake workflow forp re-processing single plane illumination microscopy (SPIM, aka lightsheet microscopy)
 
+## Requirements
+
+ - Linux system with Singularity/Apptainer installed.
+ - Python >= 3.11
+ - Lightsheet data in a folder, or in a tar file (see tif filename pattern in `config.yml`)
+
 ## Usage
 
-The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=khanlab%2Fspimprep).
+
+Clone this repository to the folder you want to run the workflow in, update the `config/datasets.tsv` to point to your dataset(s), and optionally update the `config/config.yml` with customized options. 
+
+Install dependencies with:
+```
+pip install .
+```
+
+Then, to do a dry-run use:
+```
+snakemake -np 
+```
+
+To run on all cores use:
+```
+snakemake -c all --sdm apptainer
+```
+
+### WIP:  The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/?usage=khanlab%2Fspimprep).
 
 
 Note: Designed to work with data from the Miltenyi Biotec UltraMicroscope Blaze, but could be adapted to other types of data
+
+## TODO:
+
+ - [ ] any changes to post to Snakemake Workflow Catalog, and verify usage there