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Merge pull request #12 from ttubb/dev #41

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Merge pull request #12 from ttubb/dev

Merge pull request #12 from ttubb/dev #41

Workflow file for this run

.github/workflows/python-app.yml at 01a9eb7
# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python
name: Python application
on:
push:
branches: [ "main" ]
pull_request:
branches: [ "main" ]
permissions:
contents: read
jobs:
build:
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v4
- name: Set up Python 3.10
uses: actions/setup-python@v4
with:
python-version: "3.10"
- name: Install the package and workflow as well as package dependencies
run: |
python -m pip install --upgrade pip
pip install flake8
python -m pip install .
- name: Download webin-cli
run: |
submg download_webin
- name: Lint with flake8
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Example 01
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=01_samples_reads_assembly_bins_mags.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example01/staging \
--logging_dir example01/logging \
--submit_samples \
--submit_reads \
--submit_assembly \
--submit_bins \
--submit_mags
- name: Example 02
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=02_samples_reads_assembly_bins.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example02/staging \
--logging_dir example02/logging \
--submit_samples \
--submit_reads \
--submit_assembly \
--submit_bins
- name: Example 03
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=03_samples_reads_assembly.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example03/staging \
--logging_dir example03/logging \
--submit_samples \
--submit_reads \
--submit_assembly
- name: Example 04
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=04_reads_assembly_bins_mags.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example04/staging \
--logging_dir example04/logging \
--submit_reads \
--submit_assembly \
--submit_bins \
--submit_mags
- name: Example 05
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=05_reads_assembly_bins.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example05/staging \
--logging_dir example05/logging \
--submit_reads \
--submit_assembly \
--submit_bins
- name: Example 06
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=06_reads_assembly.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example06/staging \
--logging_dir example06/logging \
--submit_reads \
--submit_assembly
- name: Example 07
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=07_assembly_bins_mags.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example07/staging \
--logging_dir example07/logging \
--submit_assembly \
--submit_bins \
--submit_mags
- name: Example 08
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=08_assembly_bins.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example08/staging \
--logging_dir example08/logging \
--submit_assembly \
--submit_bins
- name: Example 09
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=09_assembly.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example09/staging \
--logging_dir example09/logging \
--submit_assembly
- name: Example 10
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=10_bins_mags.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example10/staging \
--logging_dir example10/logging \
--submit_bins \
--submit_mags
- name: Example 11
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=11_bins.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example11/staging \
--logging_dir example11/logging \
--submit_bins
- name: Example 12
env:
ENA_USER: ${{ secrets.ENA_USER }}
ENA_PASSWORD: ${{ secrets.ENA_PASSWORD }}
run: |
cd examples
CFG=12_mags.yaml
RANDOM_STR=$(tr -dc 'A-Za-z0-9' </dev/urandom | head -c 5)
sed -i "s/idx00/${RANDOM_STR}/g" "$CFG"
submg submit \
--config $CFG \
--staging_dir example12/staging \
--logging_dir example12/logging \
--submit_mags