diff --git a/Dockerfile b/Dockerfile index bfea56bb..2d22ff46 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,14 +1,15 @@ -FROM continuumio/miniconda3 +FROM continuumio/miniconda3:4.11.0 RUN apt-get update #NOTE: I don't know whether the --fix-broken is actually needed -RUN apt-get -y install gcc libdeflate-dev libcurl4-openssl-dev --fix-broken +RUN apt-get -y install gcc zip libdeflate-dev libcurl4-openssl-dev --fix-broken -WORKDIR /cgr-dev +WORKDIR /home RUN mkdir GwasQcPipeline +RUN mkdir data -WORKDIR /cgr-dev/GwasQcPipeline +WORKDIR /home/GwasQcPipeline ENV PYTHONPATH=${PYTHONPATH}:${PWD} @@ -30,6 +31,7 @@ RUN poetry install --without dev #RUN pre-commit install #RUN pre-commit run -WORKDIR /cgr-dev + +WORKDIR /home/data ENTRYPOINT [ "cgr" ] diff --git a/README.md b/README.md index d7d389f1..fb277c55 100755 --- a/README.md +++ b/README.md @@ -27,6 +27,16 @@ If you use this workflow in a paper, please cite the URL of this repository (htt The documentation of this pipeline is at https://nci-cgr.github.io/GwasQcPipeline/ +### Deploying with Docker + +``` +docker build -t gwas_qc_pipe . +``` + +``` +docker run -v $(pwd):/home/data -i -t gwas_qc_pipe snakemake -k --use-conda -npr +``` + ### LOG - add Plink GWAS for case-controls - add `sex_chr_included` parameter to config.yml. If `false` sex concordance check step is skipped.