Functional docker container build and run with test data

NCI-CGR · Jul 24, 2023 · 738fadd · 738fadd · n8sean · Jul 24, 2023
1 parent 9d5df3a
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diff --git 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
@@ -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.