Add ncov-recombinant v0.6.1 APHL Docker Workshop #583
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erinyoung
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Feb 8, 2023
ncov-recombinant/0.6.1/Dockerfile
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| RUN apt-get update && apt-get install -y python \ | ||
| git \ | ||
| wget && \ | ||
| rm -rf /var/lib/apt/lists/* && apt-get autoclean |
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We have found that images are smaller when using --no-install-recommends
Could you adjust line 19 to
apt-get update && apt-get install --no-install-recommends -y python \
erinyoung
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Feb 8, 2023
ncov-recombinant/0.6.1/Dockerfile
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| RUN git clone https://github.com/ktmeaton/ncov-recombinant.git &&\ | ||
| cd ncov-recombinant |
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Instead of using git clone, could you download the tarball for the version you are creating an image for?
# something like
wget https://github.com/ktmeaton/ncov-recombinant/archive/refs/tags/v0.6.1.tar.gz
git clone is hard for version control
You image will also likely be smaller and more stable if you download the tarball and install it from that as well (instead of using micromamba). Did you already try that?
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Your Dockerfile built successfully and your test worked. I was going to copy the results of the tests, but it's a lot of lines. Github actions failed because your image is missing |
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Were you able to get your permissions issues figured out? |
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Unfortunately, I am still getting errors. When I explicitly state where the Snakefile should be with I get this error: |
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I was working on this today, and I actually got this to work (to a point). I tried to run the tutorial, but there's something wrong with a python script included in the repo (I keep getting type errors when I run the tutorial or other profiles). I'm currently on the mindset that we should wait until https://github.com/phac-nml/rebar has a released version and close this PR. |
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Thanks for looking into this. -Wes |
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This PR is for ncov-recombinant version 0.6.1. The dockerfile uses micromamba as the base image.
Pull Request (PR) checklist:
docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15)spades/3.12.0/Dockerfile)shigatyper/2.0.1/test.sh)spades/3.12.0/README.md)