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Merge pull request #132 from NAL-i5K/ncbi-pep-ids #7

Merge pull request #132 from NAL-i5K/ncbi-pep-ids

Merge pull request #132 from NAL-i5K/ncbi-pep-ids #7

Workflow file for this run

name: build
on: [push]
jobs:
build1-Calculating-coverage:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: "3.9"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install coveralls coverage codecov wheel
pip install .
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Test with coverage
run: |
coverage run -a ./gff3tool/bin/gff3_QC.py -g example_file/example.gff3 -f example_file/reference.fa -o error.txt
coverage run -a ./gff3tool/bin/gff3_fix.py -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3
coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt
coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -u2 example_file/u2.txt -r merged_report.txt
coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -r merged_report.txt
coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u2 example_file/u2.txt -r merged_report.txt
coverage run -a ./gff3tool/bin/gff3_merge.py -g1 example_file/new_models_w_replace.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt -noAuto
coverage run -a ./gff3tool/bin/gff3_sort.py -g example_file/example.gff3 -og example-sorted.gff3
coverage run -a ./gff3tool/bin/gff3_to_fasta.py -g example_file/example.gff3 -f example_file/reference.fa -st all -d simple -o test_sequences
- name: after success
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: |
coverage report
coveralls --service=github
codecov
build2-Checking-links:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v2
- name: Set up Ruby
uses: ruby/setup-ruby@v1
with:
ruby-version: "3.0"
bundler-cache: true # runs 'bundle install' and caches installed gems automatically
- name: Install dependencies
run: gem install awesome_bot
- name: Checking links
run: awesome_bot --allow-redirect --allow-dupe README.md docs/*.md
build3-Testing-functions:
strategy:
matrix:
os: ['ubuntu-latest', 'windows-latest', 'macos-latest']
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v2
- name: Set up Python 3.9
uses: actions/setup-python@v2
with:
python-version: "3.9"
- name: Install dependencies
run: |
python -m pip install --upgrade pip
pip install wheel
pip install --no-cache-dir gff3tool
pip install .
- name: script
run: |
gff3_QC -g example_file/example.gff3 -f example_file/reference.fa -o error.txt
gff3_fix -qc_r error.txt -g example_file/example.gff3 -og corrected.gff3
gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt
gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -u2 example_file/u2.txt -r merged_report.txt
gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u1 example_file/u1.txt -r merged_report.txt
gff3_merge -g1 example_file/new_models.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -u2 example_file/u2.txt -r merged_report.txt
gff3_merge -g1 example_file/new_models_w_replace.gff3 -g2 example_file/reference.gff3 -f example_file/reference.fa -og merged.gff -r merged_report.txt -noAuto
gff3_sort -g example_file/example.gff3 -og example-sorted.gff3
gff3_to_fasta -g example_file/example.gff3 -f example_file/reference.fa -st all -d simple -o test_sequences