#+OPTIONS: ^:nil # 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 python-pyshex -- python3 bh20sequploader/main.py example/maximum_metadata_example.yaml example/sequence.fasta ``` Note that python-pyshex is packaged in http://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics so you'll need it to the GUIX_PACKAGE_PATH - see the README in that repository. E.g. ```sh env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ ~/opt/guix/bin/guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp python3 bh20sequploader/main.py --help ``` Latest successful Guix run ```sh env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-bioinformatics/ ~/opt/guix/bin/guix environment guix --ad-hoc git python openssl python-pycurl python-magic nss-certs python-pyshex python-arvados-python-client python-schema-salad minimap2 -- python3 bh20sequploader/main.py scripts/uthsc_samples/yaml/AL_UT14.yaml scripts/uthsc_samples/yaml/AL_UT14.fa ``` ### Using the Web Uploader To run the web uploader in a GNU Guix environment/container run it with something like ``` guix environment guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs --network openssl -- env FLASK_ENV=development PYTHONPATH=$PYTHONPATH:./bh20sequploader FLASK_APP=bh20simplewebuploader/main.py flask run * Serving Flask app "bh20simplewebuploader/main.py" * Environment: production WARNING: This is a development server. Do not use it in a production deployment. Use a production WSGI server instead. * Debug mode: off * Running on http://127.0.0.1:5000/ (Press CTRL+C to quit) ``` WIP: add gunicorn container Currently the full webserver container deploy command looks like ``` penguin2:~/iwrk/opensource/code/vg/bh20-seq-resource$ env GUIX_PACKAGE_PATH=~/iwrk/opensource/guix/guix-oinformatics/ ~/iwrk/opensource/guix/guix/pre-inst-env guix environment -C guix --ad-hoc git python python-flask python-pyyaml python-pycurl python-magic nss-certs python-pyshex python-pyyaml --network openssl python-pyshex python-pyshexc minimap2 python-schema-salad python-arvados-python-client --share=/export/tmp -- env TMPDIR=/export/tmp FLASK_ENV=development FLASK_APP=bh20simplewebuploader/main.py flask run ``` Note: see above on GUIX_PACKAGE_PATH. ## Run country semantic enrichment script cd bh20-seq-resource/scripts/db_enrichment edit input_location.csv guix environment guix --ad-hoc git python nss-certs python-rdflib -- python3 country_enrichment.py ## Run the tests guix package -i python-requests python-pandas python-jinja2 python -p ~/opt/python-dev . ~/opt/python-dev/etc/profile ## Run Virtuoso-ose Guix has a package for virtuoso-ose we use guix package -i virtuoso-ose -p ~/opt/virtuoso Create a data dir mkdir -p /export/virtuoso/var/lib/virtuoso/db chown $USER /export/virtuoso/var/lib/virtuoso/db Add an ini file cp ~/opt/virtuoso/var/lib/virtuoso/db/virtuoso.ini .config/ And run from the data dir cd /export/virtuoso/var/lib/virtuoso/db guix environment --ad-hoc virtuoso-ose -- virtuoso-t -f Visit http://localhost:8890/sparql