Patch for example align #80

Workflow file for this run

	name: Python package build

	on:
	push:
	branches: [ main ]
	pull_request:
	branches: [ main ]
	workflow_dispatch:
	branches: [ main ]

	jobs:
	test_python_3_10:
	name: Test Python 3.10
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python 3.10
	uses: actions/setup-python@v4
	with:
	python-version: "3.10"
	- uses: s-weigand/setup-conda@v1
	with:
	python-version: "3.10"
	activate-conda: true
	- run: conda --version
	- run: which python
	- name: Show working dir
	shell: bash
	run: ls
	- name: Add reademption bin to PATH
	shell: bash
	run: echo "bin" >> $GITHUB_PATH
	- name: Conda info
	shell: bash
	run: conda info
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install flake8 pytest
	python -m pip install matplotlib
	python -m pip install biopython
	python -m pip install pysam
	python -m pip install pandas
	python -m pip install seaborn
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Update
	shell: bash
	run: sudo apt-get update
	- name: Install packages
	shell: bash
	run: sudo apt-get install -y python3 python3-setuptools python3-pip cython3 zlib1g-dev make libncurses5-dev libxml2-dev libcurl4-openssl-dev r-base
	- name: Conda info
	shell: bash
	run: conda info
	- name: Conda install segemehl
	shell: bash
	run: conda install -c bioconda segemehl=0.3.4
	- name: Conda list
	shell: bash
	run: conda list
	- name: List conda bin
	run: ls $CONDA/bin
	- name: Add conda bin (segemehl.x) to PATH
	shell: bash
	run: echo "$CONDA/bin" >> $GITHUB_PATH
	- name: Install DESEQ2
	shell: bash
	run: sudo echo "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') ; BiocManager::install('DESeq2'); install.packages('gplots')" \| sudo R --no-save
	- name: Show python version
	shell: bash
	run: python --version
	- name: Test with pytest
	run: \|
	pytest

	test_python_3_9:
	name: Test Python 3.9
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python 3.9
	uses: actions/setup-python@v4
	with:
	python-version: 3.9
	- uses: s-weigand/setup-conda@v1
	with:
	python-version: 3.9
	activate-conda: true
	- run: conda --version
	- run: which python
	- name: Show working dir
	shell: bash
	run: ls
	- name: Add reademption bin to PATH
	shell: bash
	run: echo "bin" >> $GITHUB_PATH
	- name: Conda info
	shell: bash
	run: conda info
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install flake8 pytest
	python -m pip install matplotlib
	python -m pip install biopython
	python -m pip install pysam
	python -m pip install pandas
	python -m pip install seaborn
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Update
	shell: bash
	run: sudo apt-get update
	- name: Install packages
	shell: bash
	run: sudo apt-get install -y python3 python3-setuptools python3-pip cython3 zlib1g-dev make libncurses5-dev libxml2-dev libcurl4-openssl-dev r-base
	- name: Conda info
	shell: bash
	run: conda info
	- name: Conda install segemehl
	shell: bash
	run: conda install -c bioconda segemehl=0.3.4
	- name: Conda list
	shell: bash
	run: conda list
	- name: List conda bin
	run: ls $CONDA/bin
	- name: Add conda bin (segemehl.x) to PATH
	shell: bash
	run: echo "$CONDA/bin" >> $GITHUB_PATH
	- name: Install DESEQ2
	shell: bash
	run: sudo echo "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') ; BiocManager::install('DESeq2'); install.packages('gplots')" \| sudo R --no-save
	- name: Show python version
	shell: bash
	run: python --version
	- name: Test with pytest
	run: \|
	pytest


	test_python_3_8:
	name: Test Python 3.8
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v3
	- name: Set up Python 3.8
	uses: actions/setup-python@v4
	with:
	python-version: 3.8
	- uses: s-weigand/setup-conda@v1
	with:
	python-version: 3.8
	activate-conda: true
	- run: conda --version
	- run: which python
	- name: Show working dir
	shell: bash
	run: ls
	- name: Add reademption bin to PATH
	shell: bash
	run: echo "bin" >> $GITHUB_PATH
	- name: Conda info
	shell: bash
	run: conda info
	- name: Install dependencies
	run: \|
	python -m pip install --upgrade pip
	python -m pip install flake8 pytest
	python -m pip install matplotlib
	python -m pip install biopython
	python -m pip install pysam
	python -m pip install pandas
	python -m pip install seaborn
	if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
	- name: Update
	shell: bash
	run: sudo apt-get update
	- name: Install packages
	shell: bash
	run: sudo apt-get install -y python3 python3-setuptools python3-pip cython3 zlib1g-dev make libncurses5-dev libxml2-dev libcurl4-openssl-dev r-base
	- name: Conda info
	shell: bash
	run: conda info
	- name: Conda install segemehl
	shell: bash
	run: conda install -c bioconda segemehl=0.3.4
	- name: Conda list
	shell: bash
	run: conda list
	- name: List conda bin
	run: ls $CONDA/bin
	- name: Add conda bin (segemehl.x) to PATH
	shell: bash
	run: echo "$CONDA/bin" >> $GITHUB_PATH
	- name: Install DESEQ2
	shell: bash
	run: sudo echo "if (!requireNamespace('BiocManager', quietly = TRUE)) install.packages('BiocManager') ; BiocManager::install('DESeq2'); install.packages('gplots')" \| sudo R --no-save
	- name: Show python version
	shell: bash
	run: python --version
	- name: Test with pytest
	run: \|
	pytest

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Patch for example align #80

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Patch for example align #80

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