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bcf2wiggle.yml
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name: bcf2wiggle Testing
on:
workflow_dispatch:
push:
branches:
- main
- dev
- refactoring
paths:
- bioconvert/bcf2wiggle.py
- .github/workflows/bcf2wiggle.yml
pull_request:
branches-ignore: []
paths:
- bioconvert/bcf2wiggle.py
schedule:
- cron: '0 0 13 * *'
jobs:
build-linux:
runs-on: ubuntu-latest
strategy:
max-parallel: 5
matrix:
python: [3.8, 3.9, '3.10']
fail-fast: false
steps:
- name: install graphviz and curl
run: |
sudo apt-get update
sudo apt-get install -y graphviz-dev
sudo apt-get install libcurl4-gnutls-dev
- name: checkout git repo
uses: actions/checkout@v2
- name: conda/mamba
uses: mamba-org/provision-with-micromamba@main
with:
cache-downloads: true
environment-file: false
environment-name: installation
channels:
conda-forge,bioconda,defaults,r
extra-specs: |
python=${{ matrix.python }}
easydev
biosniff
colorlog
deeptools
gffread
pandas
biopython>=1.70
mappy
matplotlib-base
networkx
pyyaml
pysam
pyexcel
pyexcel-ods3
pyexcel-xls
pyexcel-xlsx
pyBigWig
py2bit
statsmodels
tqdm
bamtools
bcftools
bedtools
bedops
dsrc
go==1.10.3
goalign
gotree
mosdepth
pbzip2
pigz
plink
sambamba
samtools>=1.9
seqtk
seqkit
squizz
sra-tools
ucsc-wigtobigwig
ucsc-twobittofa
ucsc-fatotwobit
ucsc-bedgraphtobigwig
ucsc-bigwigtobedgraph
wiggletools
sed
mawk
xlrd
- name: Install with pip
shell: bash -l {0}
run: |
pip install .[testing]
- name: testing
shell: bash -l {0}
run: |
pytest -n 1 --cov-report term --cov=bioconvert.bcf2wiggle test/test_bcf2wiggle.py