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authorPjotr Prins2021-08-07 11:17:21 +0200
committerPjotr Prins2021-08-07 11:17:21 +0200
commit33700066452e3c5f341b790f015f85fb976d06be (patch)
treeb76bece44a374e5d6f41c6bcd6e925cde350d24b
parent64e567caaca9c56d2d5f2a1bafe01860927e2c0c (diff)
downloadgenenetwork3-33700066452e3c5f341b790f015f85fb976d06be.tar.gz
Update info on running guix container
-rw-r--r--README.md18
-rw-r--r--guix.scm11
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)