Merge pull request #248 from NCI-CGR/dev/docker_test

Dev/docker test

.pre-commit-config.yaml

@@ -2,33 +2,33 @@
 # See https://pre-commit.com/hooks.html for more hooks
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v4.0.1
+    rev: v4.4.0
     hooks:
     -   id: trailing-whitespace
     -   id: end-of-file-fixer
     -   id: check-yaml
     -   id: check-added-large-files
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.0.0
+    rev: v2.2.5
     hooks:
     -   id: codespell
 -   repo: https://github.com/psf/black
-    rev: 20.8b1
+    rev: 23.7.0
     hooks:
     -   id: black
--   repo: https://gitlab.com/PyCQA/flake8.git
-    rev: 3.9.2
+-   repo: https://github.com/PyCQA/flake8.git
+    rev: 6.0.0
     hooks:
     -   id: flake8
 -   repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v0.812
+    rev: v1.4.1
     hooks:
     -   id: mypy
--   repo: https://github.com/timothycrosley/isort
-    rev: 5.8.0
+-   repo: https://github.com/pycqa/isort
+    rev: 5.12.0
     hooks:
     -   id: isort
 -   repo: https://github.com/snakemake/snakefmt
-    rev: 0.4.0
+    rev: v0.8.4
     hooks:
     -   id: snakefmt

Dockerfile

@@ -0,0 +1,37 @@
+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 zip libdeflate-dev libcurl4-openssl-dev --fix-broken
+
+WORKDIR /home
+
+RUN mkdir GwasQcPipeline
+RUN mkdir data
+
+WORKDIR /home/GwasQcPipeline
+
+ENV PYTHONPATH=${PYTHONPATH}:${PWD}
+
+COPY . .
+
+#NOTE: I don't think we need a special env inside the container
+#RUN conda create -n cgr-dev python=3.8 poetry make -y
+#RUN echo "conda activate cgr-dev" >> ~/.bashrc
+#RUN conda init bash && conda activate cgr-dev
+
+RUN conda install poetry make -y
+RUN conda install -c conda-forge mamba
+RUN poetry config virtualenvs.create false
+RUN poetry install --without dev
+
+#NOTE: Aren't these also not needed? Unless somehow the docs adds the help for the CLI...
+#RUN make -C docs html
+#RUN pytest -v
+#RUN pre-commit install
+#RUN pre-commit run
+
+
+WORKDIR /home/data
+
+ENTRYPOINT [ "cgr" ]

README.md

@@ -27,6 +27,25 @@ 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
+Build docker image from within GwasQcPipeline directory
+```
+docker build -t gwas_qc_pipe .
+```
+
+Test docker image if you have test data
+```
+docker run -v $(pwd):/home/data -i -t gwas_qc_pipe snakemake -k --use-conda -npr
+```
+
+Pull docker image into a singularity image file (assumes singlurity is installed)
+```
+docker run -d -p 5000:5000 --restart=always --name registry registry:2
+docker tag gwas_qc_pipe localhost:5000/gwas_qc_pipe
+docker push localhost:5000/gwas_qc_pipe
+SINGULARITY_NOHTTPS=1 singularity pull cgr_gwas_qc_pipe.sif docker://localhost:5000/gwas_qc_pipe:latest
+```
+
 ### LOG
 - add Plink GWAS for case-controls
 - add `sex_chr_included` parameter to config.yml. If `false` sex concordance check step is skipped.

pyproject.toml

@@ -23,7 +23,7 @@ python = "^3.8"
 typer = "^0.3.2"
 pandas = "^1.2.4"
 snakemake = "~6.15.5"
-pysam = "^0.16.0"
+pysam = "^0.21.0"
 ryd = "^0.4.1"
 pydantic = "^1.8.2"
 networkx = "^2.5"