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conda recipe

conda recipe #798

Workflow file for this run

name: conda recipe
# Controls when the workflow will run
on:
# Triggers the workflow on schedule but only for the default branch (which is master)
schedule:
- cron: '0 7 * * 1-5'
# Allows you to run this workflow manually from the Actions tab
workflow_dispatch:
# A workflow run is made up of one or more jobs that can run sequentially or in parallel
jobs:
# This workflow contains a single job called "check_recipe"
check_recipe:
name: test bioconda recipes on ${{ matrix.os }} with python ${{ matrix.python-version }}
runs-on: ${{ matrix.os }}
strategy:
matrix:
os: ['ubuntu-latest','macos-13']
python-version: ['3.8','3.9','3.10']
# Steps represent a sequence of tasks that will be executed as part of the job
steps:
# Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it
- uses: actions/checkout@v4
# Setting up miniconda
- uses: conda-incubator/setup-miniconda@v3
with:
python-version: ${{ matrix.python-version }}
channels: bioconda,conda-forge,anaconda,defaults
activate-environment: test
- name: Set up test environment
shell: bash -l {0}
run: |
conda install -y ppanggolin
- name: check installation
shell: bash -l {0}
run: |
python --version
ppanggolin --version
- name: all workflow run
shell: bash -l {0}
run: |
cd testingDataset/
ppanggolin all --cpu 1 --anno genomes.gbff.list -o pango
ppanggolin info -p pango/pangenome.h5 --content --parameters --status