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# Build dockerfile on change | ||
name: Build Docker (env/Dockerfile) | ||
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on: | ||
push: | ||
paths: | ||
- 'env/Dockerfile' | ||
- 'env/conda.yml' | ||
- '.github/workflows/build_docker.yml' | ||
pull_request: | ||
paths: | ||
- 'env/Dockerfile' | ||
- 'env/conda.yml' | ||
- '.github/workflows/build_docker.yml' | ||
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jobs: | ||
build: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v2 | ||
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# Build Tools | ||
- name: Build and Publish | ||
uses: elgohr/Publish-Docker-Github-Action@master | ||
with: | ||
name: andersenlab/heritability | ||
tag: "${{ steps.current-time.formattedTime }}" | ||
username: ${{ secrets.KSE_DOCKER_USER }} | ||
password: ${{ secrets.KSE_DOCKER_PASS }} | ||
snapshot: true | ||
dockerfile: Dockerfile | ||
workdir: "env" | ||
tags: "latest" | ||
cache: true |
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FROM continuumio/miniconda | ||
MAINTAINER Katie Evans <katiesevans9@gmail.com> | ||
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COPY conda.yml . | ||
RUN \ | ||
conda env update -n root -f conda.yml \ | ||
&& conda clean -a | ||
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RUN Rscript -e "install.packages('valr', dependencies=TRUE, repos='http://cran.us.r-project.org')" | ||
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# install other tools not avalible on conda cloud | ||
RUN apt-get --allow-releaseinfo-change update && apt-get install -y procps | ||
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RUN conda install -c conda-forge mscorefonts |
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name: heritability | ||
channels: | ||
- defaults | ||
- bioconda | ||
- r | ||
- biobuilds | ||
- conda-forge | ||
dependencies: | ||
- bcftools=1.9 | ||
- pandoc=2.12 | ||
- plink=1.90b6.12 | ||
- bedtools=2.29.2 | ||
- libiconv | ||
- r=3.6.0 | ||
- r-tidyverse=1.3.0 | ||
- r-data.table=1.12.2 | ||
#- r-DT=0.5 | ||
#- r-genetics=1.3.8.1.2 | ||
- r-boot | ||
- r-lme4 | ||
- r-futile.logger | ||
- r-knitr=1.22 | ||
- r-rmarkdown=1.12 | ||
- r-sommer=4.0.4 | ||
#- r-coop=0.6-2 |