From 628b0e296768eb7d88383ea536a93dc4860f34a2 Mon Sep 17 00:00:00 2001
From: jsanjak <jsanjak@gmail.com>
Date: Mon, 24 Jul 2023 18:29:19 +0000
Subject: [PATCH] updated with singularity commands

---
 README.md | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index fb277c55..8062d3f2 100755
--- a/README.md
+++ b/README.md
@@ -28,15 +28,24 @@ If you use this workflow in a paper, please cite the URL of this repository (htt
 The documentation of this pipeline is at https://nci-cgr.github.io/GwasQcPipeline/
 
 ### Deploying with Docker
-
+Build docker image from within GwasQcPipeline directory
 ```
 docker build -t gwas_qc_pipe .
 ```
 
+Test docker image if you have test data
 ```
 docker run -v $(pwd):/home/data -i -t gwas_qc_pipe snakemake -k --use-conda -npr
 ```
 
+Pull docker image into a singularity image file (assumes singlurity is installed)
+```
+docker run -d -p 5000:5000 --restart=always --name registry registry:2
+docker tag gwas_qc_pipe localhost:5000/gwas_qc_pipe
+docker push localhost:5000/gwas_qc_pipe
+SINGULARITY_NOHTTPS=1 singularity pull cgr_gwas_qc_pipe.sif docker://localhost:5000/gwas_qc_pipe:latest
+```
+
 ### LOG
 - add Plink GWAS for case-controls
 - add `sex_chr_included` parameter to config.yml. If `false` sex concordance check step is skipped.