From 9f8de83700a5aa1c19ec8d11b0978e8852b442db Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 25 Jan 2023 06:37:37 -0600
Subject: Some comments

---
 README.md                | 18 ++++++++++++++----
 gn3/computations/rqtl.py |  2 +-
 2 files changed, 15 insertions(+), 5 deletions(-)

diff --git a/README.md b/README.md
index 6e33e8c..f328e87 100644
--- a/README.md
+++ b/README.md
@@ -21,8 +21,6 @@ A continuously deployed instance of genenetwork3 is available at
 redeployed on every commit provided that the [continuous integration
 tests](https://ci.genenetwork.org/jobs/genenetwork3) pass.
 
-
-
 ## Installation
 
 #### GNU Guix packages
@@ -35,6 +33,8 @@ There are at least three ways to start GeneNetwork3 with GNU Guix:
 2. Create a container with `guix shell -C`
 3. Use a profile and shell settings with `source ~/opt/genenetwork3/etc/profile`
 
+At this point we use all three for different purposes.
+
 #### Create an environment:
 
 Simply load up the environment (for development purposes):
@@ -43,7 +43,7 @@ Simply load up the environment (for development purposes):
 guix shell -Df guix.scm
 ```
 
-Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up.
+Also, make sure you have the guix-bioinformatics channel set up correctly and this should work
 
 ```bash
 guix shell --expose=$HOME/genotype_files/ -Df guix.scm
@@ -51,7 +51,15 @@ python3
   import redis
 ```
 
-#### Run a Guix container
+Check if guix and guix-bioinformatics channel are up-to-date with
+
+```
+guix describe
+```
+
+#### Run a Guix container with network
+
+Containers provide full isolation from the underlying distribution. Very useful for figuring out any dependency issues:
 
 ```
 guix shell -C --network --expose=$HOME/genotype_files/ -Df guix.scm
@@ -59,6 +67,8 @@ guix shell -C --network --expose=$HOME/genotype_files/ -Df guix.scm
 
 #### Using a Guix profile (or rolling back)
 
+A guix profile is different from a Guix shell - it has less isolation from the underlying distribution.
+
 Create a new profile with
 
 ```
diff --git a/gn3/computations/rqtl.py b/gn3/computations/rqtl.py
index 2f9c4a2..f082482 100644
--- a/gn3/computations/rqtl.py
+++ b/gn3/computations/rqtl.py
@@ -1,4 +1,4 @@
-"""Procedures related rqtl computations"""
+"""Procedures related to R/qtl computations"""
 import os
 from bisect import bisect
 from typing import Dict, List, Tuple, Union
-- 
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