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author | Pjotr Prins | 2021-08-07 11:17:21 +0200 |
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committer | Pjotr Prins | 2021-08-07 11:17:21 +0200 |
commit | 33700066452e3c5f341b790f015f85fb976d06be (patch) | |
tree | b76bece44a374e5d6f41c6bcd6e925cde350d24b /README.md | |
parent | 64e567caaca9c56d2d5f2a1bafe01860927e2c0c (diff) | |
download | genenetwork3-33700066452e3c5f341b790f015f85fb976d06be.tar.gz |
Update info on running guix container
Diffstat (limited to 'README.md')
-rw-r--r-- | README.md | 18 |
1 files changed, 15 insertions, 3 deletions
@@ -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 ``` |