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Original file line number | Diff line number | Diff line change |
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# DOCKER FILE FOR WORKSHOP-RNASEQ | ||
# 2023 Roy Francis | ||
|
||
FROM rocker/verse:4.2.3 | ||
LABEL Description="Docker image for NBIS workshop-rnaseq" | ||
LABEL Maintainer="roy.francis@nbis.se" | ||
LABEL org.opencontainers.image.source="https://github.com/NBISweden/workshop-rnaseq" | ||
|
||
RUN apt-get update -y \ | ||
&& apt-get install --no-install-recommends -y \ | ||
libxml2-dev \ | ||
libssl-dev \ | ||
libcurl4-openssl-dev \ | ||
libudunits2-dev \ | ||
libopenblas-base \ | ||
libgdal-dev \ | ||
&& wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb \ | ||
&& apt-get install -y ./google-chrome-stable_current_amd64.deb \ | ||
&& rm -rf google-chrome-stable_current_amd64.deb \ | ||
&& rm -rf /var/lib/apt/lists/* \ | ||
&& Rscript -e 'install.packages(c("bookdown","knitr","remotes","fontawesome","formattable","kableExtra","leaflet","pagedown","lubridate","markdown","xaringan","yaml"),repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest");' \ | ||
&& mkdir /rmd | ||
|
||
RUN Rscript -e 'install.packages(c("BiocManager","dplyr","enrichR","ggplot2","gridExtra","pheatmap","pvclust","rafalib","stringr","tidyr","locfit"),repos = "https://packagemanager.posit.co/cran/__linux__/jammy/latest");' | ||
RUN Rscript -e 'BiocManager::install(c("DESeq2","edgeR","fgsea","biomaRt","GEOquery"));' | ||
WORKDIR /rmd | ||
CMD Rscript -e "rmarkdown::render_site()" | ||
|
||
# build container | ||
# docker build -t ghcr.io/nbisweden/workshop-rnaseq:1.0.0 . | ||
# docker tag ghcr.io/nbisweden/workshop-rnaseq:1.0.0 ghcr.io/nbisweden/workshop-rnaseq:latest | ||
|
||
# push to ghcr | ||
# docker login ghcr.io | ||
# docker push ghcr.io/nbisweden/workshop-rnaseq:1.0.0 | ||
# docker push ghcr.io/nbisweden/workshop-rnaseq:latest | ||
|
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# run container | ||
# render all files | ||
# docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest | ||
# render one file | ||
# docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest Rscript -e 'rmarkdown::render("index.Rmd")' |
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--- | ||
title: " " | ||
--- | ||
|
||
<footer class="footer"> | ||
<div class="container footer-container"> | ||
<div class="row"> | ||
|
||
<hr> | ||
|
||
<div class="col-sm-8" style="text-align:left;vertical-align:middle;"> | ||
<p class="small" style="color:#bdbdbd;"> | ||
[NBIS](https://nbis.se/) • [SciLifeLab](https://www.scilifelab.se/) | ||
</p> | ||
</div> | ||
|
||
<div class="col-sm-4" style="text-align:right;vertical-align:middle;"> | ||
<p style="color:#bdbdbd;"> | ||
<span> | ||
<span class="footericon" style="padding-right:4px; padding-left:4px"> | ||
<a href="https://nbis.se/">`r fontawesome::fa("globe-americas",fill="#bdbdbd")`</a> | ||
</span> | ||
<span class="footericon" style="padding-right:4px; padding-left:4px"> | ||
<a href="https://twitter.com/NBISwe">`r fontawesome::fa("twitter",fill="#bdbdbd")`</a> | ||
</span> | ||
<span class="footericon" style="padding-left:4px"> | ||
<a href="https://www.linkedin.com/company/nbisweden/">`r fontawesome::fa("linkedin",fill="#bdbdbd")`</a> | ||
</span> | ||
</span> | ||
</p> | ||
</div> | ||
|
||
</div> | ||
</div> | ||
</footer> |
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