Move processing pipeline to Docker #18
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Also includes a list of user installed R packages
isolated-cell-pop, NARES, and sle-wb pipelines
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LGTM
You'll probably want to add instructions to the README of how to run the pipeline using your docker image. Also, is your dockerfile on dockerhub? You may want to consider doing that and also adding docker pull info to the readme (example: https://hub.docker.com/r/gregway/hgsc_subtypes/)
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What is this line doing? What is R install2.r? Curious
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The --error flag will make it such that an error is thrown if the package installation fails (instead of a warning) (see: jsta/r-docker-tutorial#41)
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Good point about the README + documentation @gwaygenomics -- was considering filing a separate PR for that, do you think it makes more sense to include it here? Also, let me know if you think it's resolves the referenced issue. |
Up to you, I think it makes sense to do separately if that's your preference
Looks like it does, since both try to solve the same issue. May want to update within the issue your decision to use docker, for posterity. Feel free to close |
Related: #3
This pull request is moving the processing pipeline to a Docker container (
docker/Dockerfileanddocker/user_installed_R_packages.txt). This version of the container corresponds tojtaroni/multi-plier:v1. I've now run theisolated-cell-pop,NARESandsle-wbpipelines in the container (those file updates are included in this PR).Also includes:
sle-wb/02-calculate_spearman_affy_norm.R