Daily Component Tests and Migrations #457
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name: Daily Component Tests and Migrations | |
on: | |
schedule: | |
- cron: "0 9 * * *" | |
jobs: | |
build: | |
name: Daily Component Tests and Migrations (Python ${{ matrix.python-version }}) | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: [3.7] | |
fail-fast: false | |
steps: | |
- uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniconda-version: 'latest' | |
auto-update-conda: true | |
python-version: ${{ matrix.python-version }} | |
channels: conda-forge,bioconda | |
activate-environment: anvio_env | |
- name: "Set up the conda environment" | |
shell: bash -l {0} | |
run: | | |
conda info -a | |
conda install -y "mamba >=0.24.0" | |
mamba install -y python=${{ matrix.python-version }} sqlite prodigal idba mcl muscle=3.8.1551 hmmer diamond blast megahit spades bowtie2 tbb=2020.3 bwa graphviz "samtools >=1.9" trimal iqtree trnascan-se fasttree | |
mamba install -y -c conda-forge r-stringi=1.7.8 | |
mamba install -y r-base r-tidyverse r-optparse r-stringi r-magrittr r-reshape2 | |
Rscript -e 'install.packages("BiocManager", repos="https://cran.rstudio.com"); BiocManager::install("qvalue")' | |
- uses: actions/checkout@v2 | |
- name: "Install anvi'o from the codebase" | |
shell: bash -l {0} | |
run: | | |
pip install . | |
- name: "Run component tests for general metagenomics tasks" | |
shell: bash -l {0} | |
run: | | |
anvi-self-test --suite metagenomics-full --no-interactive | |
- name: "Run component tests for metabolism framework" | |
shell: bash -l {0} | |
run: | | |
anvi-self-test --suite metabolism --no-interactive | |
- name: "Migrate ancient anvi'o databases" | |
shell: bash -l {0} | |
run: | | |
anvi-self-test --suite database-migrations |