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create sequana_pipelines #13

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merged 2 commits into from
Jan 9, 2023
Merged

create sequana_pipelines #13

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3239479
create sequana_pipelines
ddesvillechabrol Jan 5, 2023
b56da33
update readme
ddesvillechabrol Jan 9, 2023
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2 changes: 2 additions & 0 deletions .github/workflows/main.yml
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Expand Up @@ -22,8 +22,10 @@ jobs:
steps:

- uses: actions/checkout@v3

- name: Install poetry
run: pipx install poetry

- name: Setup python 3.X
uses: actions/setup-python@v4
with:
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36 changes: 19 additions & 17 deletions .github/workflows/pypi.yml
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Expand Up @@ -10,30 +10,32 @@ jobs:
name: Build and publish to PyPI and TestPyPI
runs-on: ubuntu-20.04
steps:
- uses: actions/checkout@main
- name: Set up Python 3.7
uses: actions/setup-python@v1
- uses: actions/checkout@v3

- name: Set up Python 3.9
uses: actions/setup-python@v4
with:
python-version: 3.7
python-version: 3.9

- name: Install package
run: |
pip install build
- name: Install poetry
run: pipx install poetry

- name: Build source tarball
run: |
rm -rf dist;
python setup.py sdist
poetry build

- name: Config Test PyPI
run: |
poetry config repositories.testpypi https://test.pypi.org/legacy/
poetry config pypi-token.testpypi ${{ secrets.TEST_PYPI_API_KEY }}

- name: Publish distribution to Test PyPI
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.TEST_PYPI_API_TOKEN }}
repository_url: https://test.pypi.org/legacy/
run: poetry publish -r testpypi

- name: Config PyPI
run: poetry config pypi-token.pypi ${{ secrets.PYPI_API_KEY }}

- name: Publish distribution to PyPI
if: startsWith(github.ref, 'refs/tags')
uses: pypa/gh-action-pypi-publish@release/v1
with:
user: __token__
password: ${{ secrets.PYPI_API_TOKEN }}
run: poetry publish
4 changes: 2 additions & 2 deletions README.md
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Expand Up @@ -6,7 +6,7 @@
[![PyPI version](https://badge.fury.io/py/mergegi.svg)](https://badge.fury.io/py/mergegi)


**MergeGI** provides a single command line to merge and select barcoded raw data from [MGI](https://en.mgi-tech.com/products/) sequencing runs into a set of FastQ files ready for subsequent bioinformatics analysis.
**MergeGI** provides a single command line to merge and select barcoded raw data from [MGI](https://en.mgi-tech.com/products/) sequencing runs into a set of FastQ files ready for subsequent bioinformatics analysis.


- [Installation](#installation)
Expand All @@ -16,7 +16,7 @@

## Installation

We provide **MergeGI** as a Python library available on [Pypi](https://pypi.python.org). The standalone application is called **mergegi** and can be installed in an environment with Python>3.6 as follows:
We provide **MergeGI** as a Python library available on [Pypi](https://pypi.python.org). The standalone application is called **mergegi** and can be installed in an environment with Python>3.7 as follows:

pip install mergegi

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