Update chisel_nonormal_combocall.py #72
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name: CI | |
on: | |
push: | |
branches: [ master, develop, py3, ci ] | |
pull_request: | |
branches: [ master, develop, py3, ci ] | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python: [2.7.18] | |
steps: | |
- uses: actions/checkout@v2 | |
with: | |
lfs: false | |
- name: Cache Testing Data | |
id: cache-test-data | |
uses: actions/cache@v2 | |
with: | |
path: testdata | |
key: testdata | |
- name: Download Testing Data | |
if: steps.cache-test-data.outputs.cache-hit != 'true' | |
run: | | |
pip3 install wheel | |
pip3 install setuptools | |
pip3 install zenodo-get | |
python3 -m zenodo_get 10.5281/zenodo.3950299 --output-dir=testdata | |
- name: Set Testing Data Envvar | |
run: | | |
echo "TEST_DIRECTORY=$(realpath testdata)" >> $GITHUB_ENV | |
- name: Install SAMtools | |
run: | | |
wget https://sourceforge.net/projects/samtools/files/samtools/1.7/samtools-1.7.tar.bz2/download -O samtools-1.7.tar.bz2 | |
tar xvjf samtools-1.7.tar.bz2 | |
(cd samtools-1.7 && ./configure && make) | |
echo $(realpath samtools-1.7) >> $GITHUB_PATH | |
- name: Install BCFTools | |
run: | | |
wget https://sourceforge.net/projects/samtools/files/samtools/1.7/bcftools-1.7.tar.bz2/download -O bcftools-1.7.tar.bz2 | |
tar xvjf bcftools-1.7.tar.bz2 | |
(cd bcftools-1.7 && ./configure && make) | |
echo $(realpath bcftools-1.7) >> $GITHUB_PATH | |
- name: Download and index hg19.fa | |
run: | | |
wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/hg19.fa.gz --directory-prefix=${TEST_DIRECTORY} | |
(cd ${TEST_DIRECTORY} && gunzip -df hg19.fa.gz && samtools faidx hg19.fa && samtools dict hg19.fa > hg19.dict) | |
- name: Setup Python | |
uses: actions/setup-python@v2 | |
with: | |
python-version: ${{ matrix.python }} | |
- name: Install Tox and any other packages | |
run: | | |
python -m pip install coverage tox tox-gh-actions | |
- name: Test with tox | |
run: | | |
tox | |
env: | |
PLATFORM: ${{ matrix.python }} |