Create install script #37
Workflow file for this run
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| name: DevTesting | |
| on: | |
| push: | |
| branches: | |
| - master | |
| - dev | |
| pull_request: | |
| branches: | |
| - master | |
| - dev | |
| jobs: | |
| deploy: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/[email protected] | |
| - uses: docker://snakemake/snakemake:v7.19.1 | |
| with: | |
| directory: '.test' | |
| - name: dryrun | |
| shell: bash {0} | |
| run: | | |
| # TODO: install & use `carlisle init` instead of manually copying files | |
| mkdir output_carlisle | |
| for dir in workflow workflow/scripts config resources | |
| do | |
| cp -r $dir output_carlisle | |
| done | |
| mkdir output_carlisle/annotation | |
| for f in hg38.fa genes.gtf hg38.bed hg38.tss.bed hg38_refseq.ucsc Ecoli_GCF_000005845.2_ASM584v2_genomic.fna adapters.fa | |
| do | |
| touch output_carlisle/annotation/$f | |
| done | |
| # TODO: use `carlisle run --mode dryrun` | |
| docker run -v $PWD:/opt2/output_carlisle snakemake/snakemake:v7.19.1 /bin/bash -c \ | |
| "cd /opt2/output_carlisle && snakemake --dryrun --configfile .test/config_lint.yaml" |