Upload one gse #6

	name: Upload one gse

	on:
	workflow_dispatch:
	inputs:
	gse:
	description: 'gse number. ["GSE12345"]'
	required: true


	jobs:
	build:
	runs-on: ${{ matrix.os }}
	strategy:
	matrix:
	python-version: [ "3.12" ]
	os: [ ubuntu-latest ]
	steps:
	- uses: actions/checkout@v4
	- name: Set up Python
	uses: actions/setup-python@v5
	with:
	python-version: '3.x'
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	pip install uv
	uv pip install torch==2.3.1+cpu -f https://download.pytorch.org/whl/torch_stable.html --system
	uv pip install git+https://github.com/databio/bedboss.git@partial_processing#egg=bedboss --system

	- name: Do something here
	run: \|
	echo "Hello, ${{ github.actor }}"
	echo "The GSE is ${{ inputs.gse }}"

	- name: Upload Project
	run: bedboss geo upload-gse --outfolder /tmp/out --gse ${{ inputs.gse }} --no-use-skipper --light --bedbase-config config.yaml
	env:
	POSTGRES_HOST: ${{ secrets.POSTGRES_HOST }}
	POSTGRES_PASSWORD: ${{ secrets.POSTGRES_PASSWORD }}
	POSTGRES_USER: ${{ secrets.POSTGRES_USER }}
	QDRANT_HOST: ${{ secrets.QDRANT_HOST }}
	QDRANT_API_KEY: ${{ secrets.QDRANT_API_KEY }}
	AWS_ENDPOINT_URL: ${{ secrets.AWS_ENDPOINT_URL }}
	AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }}
	AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }}

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