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Maintainance/docker dev env #32

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2da226a
added development docker image
jspaezp Nov 29, 2022
1e4bc5d
added newline at end of files
jspaezp Nov 29, 2022
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8 changes: 8 additions & 0 deletions .devcontainer/Dockerfile
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FROM --platform=linux/amd64 ghcr.io/talusbio/nf-encyclopedia:latest
RUN apt update && apt install default-jdk-headless git docker -y
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@wfondrie wfondrie Nov 29, 2022

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question: Have you tried used the version of the JRE that is installed in the production image?

We build on top of the official EncyclopeDIA image, which uses the openjdk:8-jre as their base image. I don't know if the JRE version will work with NextFlow, but it might be worth checking.

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@wfondrie wfondrie Nov 29, 2022

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Here's the EncyclopeDIA Dockerfile: https://bitbucket.org/searleb/encyclopedia/src/master/Dockerfile

ENV JAVA_HOME=/usr/lib/jvm/java-1*-openjdk-amd64
ENV PATH="/usr/bin:$PATH"
RUN export -n _JAVA_OPTIONS
RUN unset _JAVA_OPTIONS ; cd /bin && curl -s https://get.nextflow.io | bash

8 changes: 8 additions & 0 deletions .devcontainer/devcontainer.json
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{
"build": { "dockerfile": "Dockerfile" },

"customizations": {
"vscode": {}
}
Comment on lines +4 to +6
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@wfondrie wfondrie Nov 29, 2022

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question: What does this customization do?

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@jspaezp jspaezp Nov 29, 2022

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This is a placeholder for vscode plugins .... can be removed
Nontheless, the whole impact of this PR is reduced by #35

}