Adding Dr. PRG #776
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Adding Dr. PRG #776
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Closes #762 |
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@erinyoung, why don't you start with staphb/bcftools:1.18 as "builder" and build other tools in it? Its base is jammy, too. This way, you will have fewer layers. |
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Why? Legacy reasons. The first "builder" was originally built on a rust base. Generally I get things working, and then I clean them up. This one isn't working. I just tried building from the bcftools image as the first base, and it still doesn't work. Doesn't seem to add any extra errors, though. |
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This PR is now ready to review. Turns out Dr. PRG has dependencies that aren't listed. The first hidden missing dependency that I found was for htslib. I added in htslib, but continued to run into issues. My error message was still the same, however, so it was not clear as to what was missing. I have given up building a smaller image and I am using a conda install instead. I also tried creating the image from the Dockerfile in the Dr. PRG repo. I had to make a small change by replacing COPY with RUN wget, but that Dockerfile did not build successfully either. This was the modified Dockerfile This was the error when I tried to build from that Dockerfile |
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It seems it is pretty complex to build from scratch. Thank you for trying! I am merging this PR... |
Kincekara
approved these changes
Nov 16, 2023
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Thank you for your PR! You can check the status of the deploy here: https://github.com/StaPH-B/docker-builds/actions/runs/6896754243 |
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This is for Dr. PRG, another tool for assessing antimicrobial resistance in TB. This is currently set as a draft so that I remember to finish this. It's missing a README plus other features.
EDIT : This PR is now ready for review!
This Dockerfile has three stages and a cheat from the bcftools image hosted by StaPH-B. Dr. PRG and its dependencies are downloaded as binaries in builder, staphb/bcftools is used in builder2, and the relevant executables from builder and builder2 are copied into the 'app' stage. Mafft is then installed in the 'app' stage.
In the test stage, I opted to download some fastq files from the ENA. I think Dr. PRG comes with tests, but I ran out of time looking how to implement them.
My current test is known to not run successfully. This is the error:
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)