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add skani 0.2.2 #1037

Merged
merged 2 commits into from
Aug 28, 2024
Merged

add skani 0.2.2 #1037

merged 2 commits into from
Aug 28, 2024

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Kincekara
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Skani has a new version including a new feature and bugfixes. I also updated rust builder image and cleaned up readme comments

diff skani/0.2.1/Dockerfile skani/0.2.2/Dockerfile 
1c1
< ARG SKANI_VER="0.2.1"
---
> ARG SKANI_VER="0.2.2"
4c4
< FROM rust:1.67 as builder
---
> FROM rust:1.80.1 AS builder
15c15
< FROM ubuntu:jammy as app
---
> FROM ubuntu:jammy AS app
41c41
< FROM app as test
---
> FROM app AS test

Pull Request (PR) checklist:

  • Include a description of what is in this pull request in this message.
  • 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 )
  • 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)
    • (optional) All test files are located in same directory as the Dockerfile (i.e. shigatyper/2.0.1/test.sh)
  • Create a simple container-specific README.md in the same directory as the Dockerfile (i.e. spades/3.12.0/README.md)
    • If this README is longer than 30 lines, there is an explanation as to why more detail was needed
  • Dockerfile includes the recommended LABELS
  • Main README.md has been updated to include the tool and/or version of the dockerfile(s) in this PR
  • Program_Licenses.md contains the tool(s) used in this PR and has been updated for any missing

@Kincekara Kincekara marked this pull request as ready for review August 22, 2024 14:17
@erinyoung
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The tests worked

#13 [test 2/2] RUN skani dist e.coli-EC590.fasta e.coli-K12.fasta
#13 0.093 [00:00:00.000] (7fb9e99dd080) INFO   skani dist e.coli-EC590.fasta e.coli-K12.fasta
#13 0.136 [00:00:00.043] (7fb9e99dd080) INFO   Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs.
#13 0.136 [00:00:00.043] (7fb9e99dd080) INFO   Generating sketch time: 0.043402895
#13 0.146 [00:00:00.053] (7fb9e99dd080) INFO   ANI calculation time: 0.009702218
#13 0.146 Ref_file	Query_file	ANI	Align_fraction_ref	Align_fraction_query	Ref_name	Query_name
#13 0.146 e.coli-K12.fasta	e.coli-EC590.fasta	99.39	91.89	92.46	NC_007779.1 Escherichia coli str. K-12 substr. W3110, complete sequence	NZ_CP016182.2 Escherichia coli strain EC590 chromosome, complete genome

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@erinyoung erinyoung left a comment

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I have no changes to recommend

I am going to

  1. merge this PR
  2. deploy this to dockerhub and quay using the tag '0.2.2'
  3. overwrite the 'latest' tag

@erinyoung erinyoung merged commit c2a3397 into StaPH-B:master Aug 28, 2024
2 checks passed
@Kincekara Kincekara deleted the skani branch September 19, 2024 13:55
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2 participants