update Makefile with CC flags #16

	name: starfish build

	# This workflow is triggered on pushes to the repository.
	on:
	push:
	branches:
	- main # Trigger the workflow on push to the main branch

	jobs:
	build:
	# This job runs on the latest Ubuntu runner hosted by GitHub Actions
	runs-on: ubuntu-latest

	steps:
	- name: Checkout Repository
	uses: actions/checkout@v2
	# This step checks out a copy of your repository.

	- name: Setup Miniconda
	uses: conda-incubator/setup-miniconda@v2
	with:
	activate-environment: starfish_build_env
	python-version: 3.8 # Specify the version of Python you need
	auto-activate-base: true
	# This step sets up Miniconda with a specific Python version.

	- name: Conda Build
	run: \|
	conda config --add channels bioconda
	conda config --add channels conda-forge
	conda install -c conda-forge conda-build conda-verify gcc_linux-64
	conda build .
	# This step installs conda-build and then uses it to build your Conda package.

	- name: Upload starfish Package
	run: \|
	conda install -c anaconda anaconda-client
	PACKAGE_FILES=($(find /usr/share/miniconda/conda-bld/linux-64/ -name "starfish*.tar.bz2"))
	NUM_FILES=${#PACKAGE_FILES[@]}

	if [ "$NUM_FILES" -eq 0 ]; then
	echo "Error: No starfish package files found."
	exit 1
	elif [ "$NUM_FILES" -gt 1 ]; then
	echo "Error: Multiple starfish package files found."
	exit 1
	fi

	echo "Uploading ${PACKAGE_FILES[0]}..."
	conda run anaconda -t ${{ secrets.ANACONDA_API_TOKEN }} upload --force "${PACKAGE_FILES[0]}"

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