From e0e9f125ccb4a91e0a2fe28b2474e6043bee63a3 Mon Sep 17 00:00:00 2001
From: John Lafin <john.lafin@utsouthwestern.edu>
Date: Tue, 17 Sep 2024 13:51:10 -0500
Subject: [PATCH] Add license and readme

---
 LICENSE   | 21 +++++++++++++++++++++
 README.md | 18 ++++++++++++++++++
 2 files changed, 39 insertions(+)
 create mode 100755 LICENSE
 create mode 100755 README.md

diff --git a/LICENSE b/LICENSE
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+++ b/LICENSE
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+MIT License
+
+Copyright (c) 2024 The University of Texas Southwestern Medical Center
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
diff --git a/README.md b/README.md
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+++ b/README.md
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+# Analysis code for "A cellular atlas of the healthy human adult female urethra"
+
+## Overview
+
+This repository contains the code necessary to replicate the analysis carried out in the above listed manuscript.
+
+## Usage
+
+1. Clone this repo and change into the directory.
+2. Launch R. If `renv` is not installed, it will be bootstrapped.
+3. Prepare the R analysis environment by running `renv::restore()`.
+4. Acquire the raw data (fastq files).
+5. Run Cell Ranger Count with version and parameters matching `run_cellranger_count.slurm`.
+6. Run CellBender with the image version and parameters matching `run_cellbender.slurm`.
+7. (Optional) Install the cellbender conda environment matching `environment_cellbender.yml`, and run `calc_rho_from_cellbender.slurm` to calculate contamination fractions.
+8. Run `01_initial_analysis.R`, modifying the input and output lines as necessary.
+9. Run `02_preprocess.R`, modifying the input and output lines as necessary.
+10. Run `03_lineage_filtering.R`, modifying the input and output lines as necessary.
-- 
GitLab