From 4808ae57ac83ef00e679c94fe6844c72f18735b9 Mon Sep 17 00:00:00 2001
From: Frederick Muriuki Muriithi
Date: Wed, 11 May 2022 05:36:30 +0300
Subject: Document generating and running qc for/with docker

---
 README.org | 54 ++++++++++++++++++++++++++++++++++++++++++++++++++----
 1 file changed, 50 insertions(+), 4 deletions(-)

diff --git a/README.org b/README.org
index 8162617..390320a 100644
--- a/README.org
+++ b/README.org
@@ -100,9 +100,29 @@ To check for correct type usage in the application, run:
   mypy --show-error-codes .
 #+END_SRC
 
-** Running QC
+** Deploying/Installing QC
+
+*** CLI: Docker
+
+Generate the docker image file with
+#+BEGIN_SRC shell
+guix pack -f docker -S /bin=bin genenetwork-qc
+#+END_SRC
+
+That creates the image file with a path such as:
+#+BEGIN_EXAMPLE
+/gnu/store/ibz5qlwzv0lyply2by7422z0c6jfaa6s-genenetwork-qc-docker-pack.tar.gz
+#+END_EXAMPLE
+
+You can now load this file into docker withe
+#+BEGIN_SRC shell
+docker load < /gnu/store/ibz5qlwzv0lyply2by7422z0c6jfaa6s-genenetwork-qc-docker-pack.tar.gz
+#+END_SRC
+
+and from there, you can run the application as detailed in the
+[[#run-cli-version][Running QC: CLI-Version]] section below
 
-*** Installing QC
+*** CLI: Guix
 
 The application can be installed using guix by pointing to the [[./guix.scm][guix.scm]] file as
 follows:
@@ -110,9 +130,16 @@ follows:
 guix package [-p /path/to/qc/profile] -f guix.scm
 #+END_SRC
 
-Once installed, the sections that follow show how to use the *qc* application
+*** Web-Version
+
+**** TODO Document deployment details for the web version of GeneNetwork QC better
+
+** Running QC
 
 *** Command-Line Version
+:PROPERTIES:
+:CUSTOM_ID: run-cli-version
+:END:
 
 Install the application as shown in the [[Installing QC]] section above.
 
@@ -136,4 +163,23 @@ qc --help
 
 *** Web Version
 
-Coming soon...
+**** TODO Document usage of the web-UI version of the application
+
+*** Docker
+
+Download the docker image file from [[https://git.genenetwork.org/fredmanglis/gnqc_py/releases][the releases page]] of the application and
+load it to docker with something like:
+#+BEGIN_SRC shell
+  docker load < genenetwork-qc-0.0.1-1-oxu472i-docker.tar.gz
+#+END_SRC
+replacing ~genenetwork-qc-0.0.1-1-oxu472i.tar.gz~ with the actual name of the
+release you downloaded
+
+Run the application with something like:
+#+BEGIN_SRC shell
+docker run -v /path/to/qnqc_py/tests/test_data:/data -ti \
+    genenetwork-qc:latest /bin/qc average /data/average_error_at_end_200MB.tsv
+#+END_SRC
+replacing ~/path/to/qnqc_py/tests/test_data~ with the path to the folder where
+the file you want to check is in, and ~average_error_at_end_200MB.tsv~ with the
+name of the file you want to check for errors.
-- 
cgit v1.2.3