Update ASM scripts #92
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# Workflow derived from https://github.com/r-lib/actions/tree/master/examples | |
# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
on: | |
push: | |
branches: [main, master, wgbs] | |
pull_request: | |
branches: [main, master, wgbs] | |
name: setup_camdac | |
jobs: | |
R-CMD-check: | |
runs-on: ubuntu-latest | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
R_KEEP_PKG_SOURCE: yes | |
steps: | |
- uses: actions/checkout@v3 | |
- uses: r-lib/actions/setup-r@v2 | |
with: | |
use-public-rspm: true | |
extra-repositories: 'https://bioconductor.org/packages/3.16/bioc' | |
- uses: r-lib/actions/setup-pandoc@v2 | |
with: | |
pandoc-version: '2.17.1' | |
- run: echo "# Test | pandoc -t html" | |
- uses: r-lib/actions/setup-r-dependencies@v2 | |
- uses: r-lib/actions/check-r-package@v2 | |
with: | |
error-on: '"error"' | |
# pipeline_files: | |
# needs: R-CMD-check | |
# runs-on: ubuntu-latest | |
# env: | |
# GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
# R_KEEP_PKG_SOURCE: yes | |
# steps: | |
# - name: Cache pipeline files | |
# id: cache-camdac | |
# uses: actions/cache@v3 | |
# env: | |
# cache-name: cache-camdac | |
# with: | |
# path: pipeline_files | |
# key: ${{ runner.os }}-camdac-${{ hashFiles('inst/extdata/pipeline_files_urls.txt') }} | |
# restore-keys: | | |
# ${{ runner.os }}-camdac-${{ env.cache-name }}- | |
# - name: Load cached files | |
# if: steps.cache-camdac.outputs.cache-hit != 'true' | |
# run: | | |
# echo "Downloading cache" | |
# Rscript -e 'devtools::load_all();download_pipeline_files("wgbs", "./pipline_files/")' | |
# Rscript -e 'devtools::load_all();download_pipeline_files("rrbs", "./pipline_files/")' | |
# - name: Restore cached data | |
# if: steps.cache-data-txt.outputs.cache-hit == 'true' | |
# run: echo "Restoring cached data" |