https://github.com/sequana/sequana_pipeline_template
a cookiecutter sequana pipeline template
https://github.com/sequana/sequana_pipeline_template
Last synced: 4 months ago
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a cookiecutter sequana pipeline template
- Host: GitHub
- URL: https://github.com/sequana/sequana_pipeline_template
- Owner: sequana
- License: bsd-3-clause
- Created: 2019-11-22T22:13:35.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2024-08-08T08:15:56.000Z (almost 2 years ago)
- Last Synced: 2025-02-18T00:51:26.809Z (over 1 year ago)
- Language: Python
- Size: 88.9 KB
- Stars: 0
- Watchers: 4
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.rst
- License: LICENSE
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README
=========================
Sequana Pipeline Template
=========================
:version: 2.0
This repository is a Cookiecutter template to start a new `Sequana pipeline `_
implementation from scratch.
Quickstart
----------
You first need to install the latest version of **cookiecutter** if you haven't installed it yet (requires
Cookiecutter 1.4.0 or higher)::
pip install -U cookiecutter
Then, no need to install the sequana_pipeline_template package itself. You can call it directly from github as
follows::
cookiecutter https://github.com/sequana/sequana_pipeline_template.git
you will be asked some questions in particular the name of the package. You can
change things later on. Except the name, most entries are populated in the
setup.py file.
- The first question asks the name of the future pipeline. There is no strict
convention in Sequana but we usually use small caps and underscores to separate
words (e.g., sequana_rnaseq).
- The second question is the short description that will be added to your
setup.py configuration file
- The third questions asked for keywords, also added to the setup.py
That's it.
If your pipeline is called **varseq**, you should end up with a structure in the
directory **sequana_varseq** similar to ::
similar to ::
├── test
│ └── __init__.py
├── doc
│ ├── conf.py
│ ├── index.rst
│ └── Makefile
├── README.rst
├── requirements.txt
├── sequana_pipelines
│ └── varseq
│ ├── config.yaml
│ ├── __init__.py
│ ├── main.py
│ ├── varseq.rules
│ ├── README.rst
│ ├── requirements.txt
│ └── schema.yaml
│ └── data
│ ├── __init__.py
├── setup.cfg
└── setup.py
You can install this new pipeline as follows::
cd sequana_varseq
python setup.py install
You can build the documentation as follows::
cd sequana_varseq/doc
make html # under linux
Or test it::
cd sequana_varseq
pytest # this tool (pytest) must be install first (pip install pytest)
Of course, you now need to work a little bit by replacing the content of some
files with your code and/or documentation and tests.
The most important editing steps are then:
1. to edit the *config.yaml* and *varseq.rules* in the sequana_pipelines/varseq
directory with your own snakemake pipeline and configuration file.
2. edit the main script **main.py** and adapt it to your needs. This will be the
entry point of the user.
3. the documentation in ./doc
4. test in ./test
5. update the requirements.txt file in varseq/ directory to add any external
dependencies. The requirements.txt at the top level is only for Python
dependencies. In principle it depends only on sequana
Once done, create a repository on https://github.com/sequana/sequana_varseq and
upload your files.
This is not perfect and we will most probably edit this template in the future
to make it more robust and possibly add such features (help needed).
Once happy, you can create a local repository::
git init
Create and switch to main branch: if you are on a different branch,
you can create and switch to the main branch with::
git checkout -b main
Add and commit changes: ensure you have at least one commit in your
repository. Make an initial commit::
git add .
git commit -m "Initial commit"
Push to Remote Repository: try pushing to the remote repository::
git remote add origin git@github.com:sequana/your_repo
git push -u origin main
Changelog
* v2: uses poetry
* v1: uses setuptools