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self-hosted.yml
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name: Self-hosted CI
on:
pull_request:
branches: [ master ]
paths-ignore:
- '**.md'
workflow_dispatch:
jobs:
check-prerequisites:
name: Check prerequisites
runs-on: [self-hosted, kmc]
env:
DATA_DIR: ../../../../data
SCRIPT: tests/kmc_CLI/check-prerequisites.py
steps:
- name: Check prerequisites
run: |
chmod +x $SCRIPT
/usr/bin/time -v $SCRIPT $DATA_DIR
prepare-small-fastq-tests:
name: Prepare small fastq tests
runs-on: [self-hosted, kmc]
env:
TRIVIAL_COUNTER: tests/kmc_CLI/trivial-k-mer-counter/bin/counter
DATA_DIR: ../../../../data
SCRIPT: tests/kmc_CLI/prepare_small_fastq_tests.py
FILE_TO_GET_PART_FROM: F.vesca/SRR072005.fastq.gz
steps:
- name: Compile trivial counter
run: |
(cd tests/kmc_CLI/trivial-k-mer-counter; /usr/bin/time -v make)
- name: Prepare pattern data
run: |
chmod +x $SCRIPT
/usr/bin/time -v $SCRIPT $DATA_DIR $TRIVIAL_COUNTER $FILE_TO_GET_PART_FROM 400000
make-tests:
name: Make tests
runs-on: [self-hosted, kmc]
needs: check-prerequisites
env:
KMC_EXE: ./bin/kmc
KMC_DUMP_EXE: ./bin/kmc_dump
KMC_TOOLS: ./bin/kmc_tools
steps:
- uses: actions/checkout@v2
with:
submodules: recursive
- name: make (default)
run: |
/usr/bin/time -v make -j32
small-fastq-tests:
name: Small fastq tests
runs-on: [self-hosted, kmc]
needs: [make-tests, prepare-small-fastq-tests]
env:
DATA_DIR: ../../../../data
SCRIPT: tests/kmc_CLI/run_small_fastq_tests.py
KMC_EXE: ./bin/kmc
KMC_DUMP_EXE: ./bin/kmc_dump
KMC_TOOLS: ./bin/kmc_tools
steps:
- name: Run all small fastq tests
run: |
chmod +x $SCRIPT
/usr/bin/time -v $SCRIPT $DATA_DIR $KMC_EXE $KMC_TOOLS $KMC_DUMP_EXE