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Update chisel_nonormal_combocall.py #72

Update chisel_nonormal_combocall.py

Update chisel_nonormal_combocall.py #72

Workflow file for this run

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 }}