Update artic for new medaka models

erinyoung commented 3 months ago

There isn't a new version of artic, but there is a new version of medaka.

Artic is showing its age. Originally, 1) the github repo was downloaded, 2) the environmental file was used to create a conda environment, 3) pip was used to install artic. I kept running into environment incompatibilities, so this image now uses micromamba to install artic entirely and the github archive is downloaded only for testing.

The medaka on conda (and installed in the step above) is an old version, and I'm most interested in the new medaka models. I do like how conda installs all of medaka's dependencies, though, even if its for an old version. Therefore, there is a reinstall of medaka using pip afterward followed by a pip install of pyabpoa. I do not fully know why pyabpoa needs to be installed last, but there are errors thrown if installed with the same line of medaka. pyabpoa does not get installed with conda for whatever reason.

Pull Request (PR) checklist:

[X] Include a description of what is in this pull request in this message.
[X] The dockerfile successfully builds to a test target for the user creating the PR. (i.e. docker build --tag samtools:1.15test --target test docker-builds/samtools/1.15 )
[X] Directory structure as name of the tool in lower case with special characters removed with a subdirectory of the version number (i.e. spades/3.12.0/Dockerfile)
- [X] (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
[X] Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
- [X] If this README is longer than 30 lines, there is an explanation as to why more detail was needed
[X] Dockerfile includes the recommended LABELS
[X] Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
[X] Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

erinyoung commented 3 months ago

@jessicarowell , it looks like adjusting the base image back to 1.4.8 resolved the issue.

jessicarowell commented 3 months ago

Built and tested successfully!

#16 sha256:14726c8f78342865030f97a8d3492e2d1a68fbd22778f9a31dc6be4b4f12a9bc 13.63MB / 31.42MB 0.2s
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#16 sha256:f44123b607d41a6ff5e3e2934fcb8f3b6121750c954020a7faea405c1a4cf535 4.55kB / 4.55kB done
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#16 sha256:bf9cfdb98097403328f35cda87e4956b1e9c748a5de09c[168](https://github.com/StaPH-B/docker-builds/actions/runs/9290571182/job/25652842303?pr=984#step:8:173)cacf0ffc508632e 683B / 683B done
#16 extracting sha256:bf9cfdb98097403328f35cda87e4956b1e9c748a5de09c168cacf0ffc508632e done
#16 sha256:87bcfcd4e3d942fd007f334bb07c32b0147ad0f5c5bb2ff1a7523c529770cdee 641B / 641B done
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#16 sha256:fc3edf513487fc003623af5b960c953f3f2e9ffd4a43aaab92d9bffc0f8de408 345B / 345B done
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#16 sha256:6c8b9e3eea7cc9e090ba9cf0250a6e26517272ae74acc46691d69cd40390553f 13.63MB / 110.32MB 0.2s
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#16 sha256:879c504f11dde80f48fb0b334593dc9ab4a67b99b4db8e95a30797208c35fb48 360.71MB / 824.68MB 4.1s
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#16 sha256:879c504f11dde80f48fb0b334593dc9ab4a67b99b4db8e95a30797208c35fb48 511.71MB / 824.68MB 5.9s
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#16 extracting sha256:879c504f11dde80f48fb0b334593dc9ab4a67b99b4db8e95a30797208c35fb48 47.6s done
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#16 sha256:76e48e988feaec29f93bc82618eea72d932e8599fb4fef6d90ff7f03c2de5af8 12.58MB / 1.45GB 0.2s
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#16 sha256:76e48e988feaec29f93bc82618eea72d932e8599fb4fef6d90ff7f03c2de5af8 335.54MB / 1.45GB 3.9s
#16 sha256:76e48e988feaec29f93bc82618eea72d932e8599fb4fef6d90ff7f03c2de5af8 416.28MB / 1.45GB 4.8s
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#16 sha256:76e48e988feaec29f93bc82618eea72d932e8599fb4fef6d90ff7f03c2de5af8 586.15MB / 1.45GB 6.6s
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#16 sha256:20042c2c42be810da6b54520fbbc2e0326a47b1b34f98cc4e5aaeba4de2ab266 9.75MB / 9.75MB 0.1s done
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#16 sha256:b0fd4f688777fe6b5d0bb54d347b884506f0c5f61871f0f9f205d158dfb74496 94B / 94B done
#16 extracting sha256:b0fd4f688777fe6b5d0bb54d347b884506f0c5f61871f0f9f205d158dfb74496 done
#16 sha256:661b3c82d2ed035f2feaa1c56c7d46d304982199c3d2abdfbd332d861756b446 13.63MB / 70.55MB 0.1s
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#16 extracting sha256:661b3c82d2ed035f2feaa1c56c7d46d304982199c3d2abdfbd332d861756b446 0.3s done
#16 CACHED

#17 exporting to docker image format
#17 exporting layers done
#17 exporting manifest sha256:f67bee20a6f57bd5ce841845245a7b8b99f150779de32815c1e25161b4a2cdf1 done
#17 exporting config sha256:8ba868ba5ee4555d767c740fa82bf0830b0644d5dbee3cb3c20f4216266b0df8 done
#17 sending tarball
#17 ...

#18 importing to docker
#18 loading layer 63290f9c9e52 327.68kB / 31.42MB
#18 loading layer cbc9e08f1de7 32.77kB / 115.22kB
#18 loading layer fc28ad0e4478 65.54kB / 5.70MB
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#18 loading layer 8b60673e34d8 557.06kB / 110.32MB
#18 loading layer 8b60673e34d8 74.09MB / 110.32MB 2.1s
#18 loading layer 1739bdb30d3a 557.06kB / 824.68MB
#18 loading layer 1739bdb30d3a 110.85MB / 824.68MB 2.1s
#18 loading layer 1739bdb30d3a 220.04MB / 824.68MB 8.2s
#18 loading layer 1739bdb30d3a 230.62MB / 824.68MB 14.9s
#18 loading layer 1739bdb30d3a 293.57MB / 824.68MB 19.0s
#18 loading layer 1739bdb30d3a 347.05MB / 824.68MB 21.0s
#18 loading layer 1739bdb30d3a 374.34MB / 824.68MB 28.3s
#18 loading layer 1739bdb30d3a 431.72MB / 824.68MB 32.4s
#18 loading layer 1739bdb30d3a 508.59MB / 824.68MB 34.5s
#18 loading layer 1739bdb30d3a 596.61MB / 824.68MB 36.6s
#18 loading layer 1739bdb30d3a 651.76MB / 824.68MB 46.5s
#18 loading layer 1739bdb30d3a 682.95MB / 824.68MB 53.6s
#18 loading layer 1739bdb30d3a 791.02MB / 824.68MB 58.4s
#18 loading layer 5f70bf18a086 32B / 32B 66.0s
#18 loading layer e7bf06040423 557.06kB / 1.45GB
#18 loading layer e7bf06040423 358.74MB / 1.45GB 2.0s
#18 loading layer e7bf06040423 718.60MB / 1.45GB 4.1s
#18 loading layer e7bf06040423 801.05MB / 1.45GB 6.1s
#18 loading layer e7bf06040423 877.92MB / 1.45GB 10.4s
#18 loading layer e7bf06040423 963.15MB / 1.45GB 12.4s
#18 loading layer e7bf06040423 1.15GB / 1.45GB 14.5s
#18 loading layer e7bf06040423 1.38GB / 1.45GB 16.6s
#18 loading layer 5f70bf18a086 32B / 32B 87.5s
#18 loading layer 7982b058a061 98.30kB / 9.75MB
#18 loading layer 8af1d80b7265 94B / 94B
#18 loading layer 0db692eea811 557.06kB / 70.55MB
#18 loading layer b8986f5092ed 285B / 285B 88.7s done
#18 loading layer 63290f9c9e52 327.68kB / 31.42MB 92.5s done
#18 loading layer cbc9e08f1de7 32.77kB / 115.22kB 91.3s done
#18 loading layer fc28ad0e4478 65.54kB / 5.70MB 88.8s done
#18 loading layer 5f70bf18a086 32B / 32B 88.7s done
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#18 loading layer 9e6d6d74b072 345B / 345B 88.7s done
#18 loading layer 8b60673e34d8 74.09MB / 110.32MB 88.6s done
#18 loading layer 1739bdb30d3a 791.02MB / 824.68MB 84.5s done
#18 loading layer e7bf06040423 1.45GB / 1.45GB 22.7s done
#18 loading layer 7982b058a061 98.30kB / 9.75MB 1.2s done
#18 loading layer 8af1d80b7265 94B / 94B 0.9s done
#18 loading layer 0db692eea811 557.06kB / 70.55MB 0.9s done
#18 DONE 92.5s

#17 exporting to docker image format
#17 sending tarball 108.6s done
#17 DONE 108.6s

#19 exporting cache to client directory
#19 preparing build cache for export
#19 writing layer sha256:072e55e492c8f53448eed58aa077e344eccc7b40c5ea9c70dadfe6a326c434b1 0.0s done
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#19 writing layer sha256:20042c2c42be810da6b54520fbbc2e0326a47b1b34f98cc4e5aaeba4de2ab266
#19 writing layer sha256:20042c2c42be810da6b54520fbbc2e0326a47b1b34f98cc4e5aaeba4de2ab266 0.2s done
#19 writing layer sha256:2712dc90660a8ae3d5fea88bd5afd6e1063a9a666685ca3bbb96a5cd8b4f477b
#19 writing layer sha256:2712dc90660a8ae3d5fea88bd5afd6e1063a9a666685ca3bbb96a5cd8b4f477b 0.1s done
#19 writing layer sha256:3ff[170](https://github.com/StaPH-B/docker-builds/actions/runs/9290571182/job/25652842303?pr=984#step:8:175)0158b11b432c1646cdcb66e7c2170a58a17bf7ef0c4f0d904d7c310daa
#19 writing layer sha256:3ff1700158b11b432c1646cdcb66e7c2170a58a17bf7ef0c4f0d904d7c310daa done
#19 writing layer sha256:492af156d32e36bc874a7fda25517dd9cf7477f35b509392efe18a488a29a8a0 done
#19 writing layer sha256:4f4fb700ef54461cfa02571ae0db9a0dc1e0cdb5577484a6d75e68dc38e8acc1 done
#19 writing layer sha256:661b3c82d2ed035f2feaa1c56c7d46d304982199c3d2abdfbd332d861756b446
#19 writing layer sha256:661b3c82d2ed035f2feaa1c56c7d46d304982199c3d2abdfbd332d861756b446 1.3s done
#19 writing layer sha256:6c8b9e3eea7cc9e090ba9cf0250a6e265[172](https://github.com/StaPH-B/docker-builds/actions/runs/9290571182/job/25652842303?pr=984#step:8:177)72ae74acc46691d69cd40390553f
#19 writing layer sha256:6c8b9e3eea7cc9e090ba9cf0250a6e26517272ae74acc46691d69cd40390553f 2.0s done
#19 writing layer sha256:76e48e988feaec29f93bc82618eea72d932e8599fb4fef6d90ff7f03c2de5af8
#19 writing layer sha256:76e48e988feaec29f93bc82618eea72d932e8599fb4fef6d90ff7f03c2de5af8 25.5s done
#19 writing layer sha256:879c504f11dde80f48fb0b334593dc9ab4a67b99b4db8e95a30797208c35fb48
#19 writing layer sha256:879c504f11dde80f48fb0b334593dc9ab4a67b99b4db8e95a30797208c35fb48 15.0s done
#19 writing layer sha256:87bcfcd4e3d942fd007f334bb07c32b0147ad0f5c5bb2ff1a7523c529770cdee
#19 preparing build cache for export 44.8s done
#19 writing layer sha256:87bcfcd4e3d942fd007f334bb07c32b0147ad0f5c5bb2ff1a7523c529770cdee done
#19 writing layer sha256:b0fd4f688777fe6b5d0bb54d347b884506f0c5f61871f0f9f205d158dfb74496 0.0s done
#19 writing layer sha256:bf9cfdb98097403328f35cda87e4956b1e9c748a5de09c168cacf0ffc508632e done
#19 writing layer sha256:f44123b607d41a6ff5e3e2934fcb8f3b612[175](https://github.com/StaPH-B/docker-builds/actions/runs/9290571182/job/25652842303?pr=984#step:8:180)0c954020a7faea405c1a4cf535 done
#19 writing layer sha256:fc3edf513487fc003623af5b960c953f3f2e9ffd4a43aaab92d9bffc0f8de408 done
#19 writing config sha256:df327b00af8a1530d1e1bfa49847f71b005de770802edca6242ccd7065467493 done
#19 writing cache manifest sha256:9c246bc3bb48b33c30a9aa6731857ee0842bed0e632175a97ebc954fab4beed5 done
#19 DONE 44.8s

#20 resolving provenance for metadata file
#20 DONE 0.0s

StaPH-B / docker-builds

Update artic for new medaka models #984