From 33700066452e3c5f341b790f015f85fb976d06be Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 7 Aug 2021 11:17:21 +0200
Subject: Update info on running guix container

---
 README.md | 18 +++++++++++++++---
 guix.scm  | 11 +++++++++++
 2 files changed, 26 insertions(+), 3 deletions(-)

diff --git a/README.md b/README.md
index c1acba1..108dcdb 100644
--- a/README.md
+++ b/README.md
@@ -11,7 +11,7 @@ Simply load up the environment (for development purposes):
 guix environment --load=guix.scm
 ```
 
-Also, make sure you have the *guix-bioinformatics* channel set up.
+Also, make sure you have the [guix-bioinformatics](https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics) channel set up.
 
 ```bash
 env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment --load=guix.scm
@@ -22,9 +22,21 @@ python3
 Better run a proper container
 
 ```
-env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm 
+env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ ~/.config/guix/current/bin/guix environment -C --network --load=guix.scm
 ```
 
+If you get a Guix error, such as `ice-9/boot-9.scm:1669:16: In procedure raise-exception:
+error: python-sqlalchemy-stubs: unbound variable` it typically means an update to guix latest is required (i.e., guix pull):
+
+```
+guix pull
+source ~/.config/guix/current/etc/profile
+```
+
+and try again.
+
+See also instructions in [.guix.scm](.guix.scm).
+
 #### Running Tests
 
 (assuming you are in a guix container; otherwise use venv!)
@@ -71,7 +83,7 @@ virtualenv --python python3 venv
 
 ```bash
 # The --ignore-installed flag forces packages to
-# get installed in the venv even if they existed 
+# get installed in the venv even if they existed
 # in the global env
 pip install -r requirements.txt --ignore-installed
 ```
diff --git a/guix.scm b/guix.scm
index efef9c1..c18f329 100644
--- a/guix.scm
+++ b/guix.scm
@@ -17,6 +17,17 @@
 ;;; You should have received a copy of the GNU General Public License
 ;;; along with genenetwork3. If not, see https://www.gnu.org/licenses/.
 
+;; To use this file to build HEAD of gemma:
+;;
+;;   env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix build -f guix.scm
+;;
+;; After checking out the git repo
+;;   cd ~ ; git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics
+;;
+;; To get a development container (e.g., run in emacs shell).
+;;
+;;   env GUIX_PACKAGE_PATH=~/guix-bioinformatics/ guix environment -C -l guix.scm
+
 (use-modules
  (srfi srfi-1)
  (srfi srfi-26)
-- 
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