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diff --git a/doc/INSTALL.md b/doc/INSTALL.md new file mode 100644 index 0000000..d8d7f3e --- /dev/null +++ b/doc/INSTALL.md @@ -0,0 +1,49 @@ +# INSTALLATION + +Other options for running this tool. + +## GNU Guix + +### Running the CLI uploader + +Another way to install this tool is inside a [GNU Guix Environment](https://guix.gnu.org/manual/en/html_node/Invoking-guix-environment.html), which can handle installing dependencies for you + +1. **Set up and enter a Guix environment with the necessary dependencies.** After installing Guix run: + +```sh +guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs +``` + +2. **Install the tool.** From there you can follow the [user installation instructions](#installation-with-pip3---user). In brief: + +```sh +pip3 install --user schema-salad arvados-python-client +``` + +Pip installed the following modules + +``` +arvados-python-client-2.0.1 ciso8601-2.1.3 future-0.18.2 google-api-python-client-1.6.7 httplib2-0.17.1 oauth2client-4.1.3 pyasn1-0.4.8 pyasn1-modules-0.2.8 rsa-4.0 ruamel.yaml-0.15.77 six-1.14.0 uritemplate-3.0.1 ws4py-0.5.1 +``` + +3. Run the tool directly with + +```sh +guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs -- python3 bh20sequploader/main.py example/sequence.fasta example/metadata.yaml +``` + +### Using the Web Uploader + +To run the web uploader in a GNU Guix environment/container + +``` +guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-magic nss-certs --network openssl -- env FLASK_APP=bh20simplewebuploader/main.py flask run + * Serving Flask app "bh20simplewebuploader/main.py" + * Environment: production + WARNING: This is a development server. Do not use it in a production deployment. + Use a production WSGI server instead. + * Debug mode: off + * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit) +``` + +WIP: add gunicorn container |