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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 45 |
1 files changed, 29 insertions, 16 deletions
@@ -3,7 +3,17 @@ GeneNetwork3 REST API for data science and machine learning ## Installation -#### Using guix +#### GNU Guix packages + +Install GNU Guix - this can be done on every running Linux system. + +There are at least three ways to start GeneNetwork3 with GNU Guix: + +1. Create an environment with `guix environment` +2. Create a container with `guix environment -C` +3. Use a profile and shell settings with `source ~/opt/genenetwork3/etc/profile` + +#### Create an environment: Simply load up the environment (for development purposes): @@ -19,23 +29,12 @@ python3 import redis ``` -Better run a proper container +#### Run a Guix container ``` 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). #### Using a Guix profile (or rolling back) @@ -61,7 +60,21 @@ set|grep store run tests, server etc... ``` -#### Running Tests +#### Troubleshooting Guix packages + +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. Also make sure your ~/guix-bioinformatics is up to date. + +See also instructions in [.guix.scm](.guix.scm). + +## Running Tests (assuming you are in a guix container; otherwise use venv!) @@ -83,7 +96,7 @@ Running mypy(type-checker): mypy . ``` -#### Running the flask app +## Running the GN3 web service To spin up the server on its own (for development): @@ -112,7 +125,7 @@ And for the scalable production version run gunicorn --bind 0.0.0.0:8080 --workers 8 --keep-alive 6000 --max-requests 10 --max-requests-jitter 5 --timeout 1200 wsgi:app ``` -##### Using python-pip +## Using python-pip IMPORTANT NOTE: we do not recommend using pip tools, use Guix instead |