Installation

conda

conda create --name YOUR_ENV_NAME --channel conda-forge python=3.6 pyyaml boto3 sos black# black is optional, it is sort of a development dependencygit clone https://github.com/lucasrla/wsi-preprocessing-sos-workflowcd wsi-preprocessing-sos-workflowconda activate YOUR_ENV_NAME

poetry or pip

git clone https://github.com/lucasrla/wsi-preprocessing-sos-workflowcd wsi-preprocessing-sos-workflow# create and activate a virtualenv, for example:pyenv virtualenv YOUR_ENV_NAME&& pyenvlocal YOUR_ENV_NAME# install the dependencies, either with:poetry install# or:pip install -r requirements.txt# note, requirements.txt in this repository were generated via:# poetry export --without-hashes -f requirements.txt -o requirements.txt

Configuration

# edit project.TEMPLATE.yml to match your needsvim project.TEMPLATE.yml# and then save it as project.yml# make sure that ~/.sos/hosts.yml has the path to your pem_file# and that the naming of hosts matches project.ymlvim~/.sos/hosts.yml

Usage

sos run -c project.yml remote.sos -v4

License