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Minor change to readme to better reflect update to 6.0 and deprecatio… #382

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merged 4 commits into from
Sep 12, 2024
Merged

Minor change to readme to better reflect update to 6.0 and deprecatio… #382

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1a10f55
Minor change to readme to better reflect update to 6.0 and deprecatio…
mattloose Aug 26, 2024
8abc624
Merge branch 'main' into feature/readme_cleanup
Adoni5 Sep 12, 2024
2da0fb7
Allow hidden files, warn if file not found
Adoni5 Sep 12, 2024
e13e456
Include hidden files in merge
Adoni5 Sep 12, 2024
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4 changes: 3 additions & 1 deletion .github/workflows/CI.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -53,7 +53,8 @@ jobs:
with:
name: my-artifact-${{ matrix.python-version }}
path: .coverage*
if-no-files-found: ignore
if-no-files-found: warn
include-hidden-files: true

merge:
name: merge
Expand All @@ -65,6 +66,7 @@ jobs:
with:
name: coverage-data
pattern: my-artifact-*
include-hidden-files: true

coverage:
name: Combine coverage
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6 changes: 3 additions & 3 deletions README.md
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Expand Up @@ -128,9 +128,9 @@ conda env create -f development.yml
conda activate readfish_dev
```

| <h2>‼️ Important !! </h2> |
|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| MinKNOW is transitioning from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.<br/>As of MinKNOW version 5.9 and Dorado server version 7.3.9 and greater Dorado requires an alternate library, `ont-pybasecall-client-lib`.<br/>The listed `ont-pyguppy-client-lib` or `ont-pybasecaller-client-lib` version may not match the version installed on your system. To fix this, Please see this [issue](https://github.com/LooseLab/readfish/issues/221#issuecomment-1381529409), using the appropriate library. |
| <h2>‼️ Important !! </h2> |
|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
| MinKNOW has now transitioned from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.<br/>As of MinKNOW version 5.9 and Dorado server version 7.3.9 and greater Dorado required an alternate library, `ont-pybasecall-client-lib`, but guppy could still be used. <br/> As of MinKNOW 6.0 Guppy support has been deprecated and only Dorado support is provided. It is important to ensure the correct library is installed for your specific configuration and the listed `ont-pyguppy-client-lib` or `ont-pybasecaller-client-lib` version may not match the versions installed on your system. To fix this, Please see this [issue](https://github.com/LooseLab/readfish/issues/221#issuecomment-1381529409), using the appropriate library. |


[ONT's Dorado Basecall Server GPU](https://community.nanoporetech.com/downloads) should be installed and running as a server.
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