+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, which can handle installing dependencies for you

Set up and enter a Guix environment with the necessary dependencies. After installing Guix run:

guix environment -C guix --ad-hoc git python openssl python-pycurl nss-certs

Install the tool. From there you can follow the user installation instructions. In brief:

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

Run the tool directly with

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.

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

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

To update the turtle files do

guix environment -C guix --ad-hoc python python-requests raptor2 curl --network -- python3 ./scripts/update_virtuoso/check_for_updates.py cache.txt dba dba

where dba is the default password.

Run the Auspice phylo-tree viewer

Auspice is developed by the Nextstrain team and we use it for exploring the phylogenetic tree. It does not scale well beyond 5,000 SARS-CoV-2 virusses, so we need to limit the input set!

Auspice runs on a separate port.

Running on port 4001 using your repo:

Install node with Guix

~/.config/guix/current/bin/guix package -i node -p ~/opt/node

Load Guix environment variables

. ~/opt/node/etc/profile

Run server after fetching data in ./data

cd auspice
npm install --global --prefix node_modules .
env PORT=4001 ./node_modules/bin/auspice view --datasetDir ./data