Quick Start guide for HSNPipeline.
To get set up with all the requirements needed across the pipeline, you can use the requirements file provided in this repository.
To install the set of requirements:
$ pip install -r requirements.txt
Note that this will install the full set of requirements needed across the whole pipeline. If you are only using a subset of the functionality, you may with to edit this file first to only install what you wish to use.
You may want to set up a new Python environment for the HSN project that includes all the necessary functionality.
If you are using conda, you can set up a new environment following the instructions here.
Similarly, you can initialize a new environment with other tools, for example, with venv.
Regardless of which tool you use, you can create a new environment for a HSN project by initializing a new environment with a specified name and Python version, and then install the requirements file from above, after making any edits or extensions needed for you project.
To get started with a new project you first want to get a copy of the templates.
You can get a copy of the templates by running the following shell script:
$ sh get_templates.sh
After the templates are initialized, you should rename the templates to match the project, and then follow the descriptions within each template to update them. From there, you can use these templates to develop the procedures needed for the particular project.
For more guidance on using the templates, see the templates guide on the documentation website, as well as the other sections on each topic.