From 2c63712af7cd7741ed280410e77e1741300f742a Mon Sep 17 00:00:00 2001 From: mattloose Date: Thu, 12 Sep 2024 15:03:25 +0100 Subject: [PATCH] =?UTF-8?q?Minor=20change=20to=20readme=20to=20better=20re?= =?UTF-8?q?flect=20update=20to=206.0=20and=20deprecatio=E2=80=A6=20(#382)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Minor change to readme to better reflect update to 6.0 and deprecation of guppy. * Allow hidden files in upload CI action, warn if file not found * Include hidden files in merge action When did this become a thing --------- Co-authored-by: Rory Munro --- .github/workflows/CI.yml | 4 +++- README.md | 6 +++--- 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/.github/workflows/CI.yml b/.github/workflows/CI.yml index f33939c..9c9fb53 100644 --- a/.github/workflows/CI.yml +++ b/.github/workflows/CI.yml @@ -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 @@ -65,6 +66,7 @@ jobs: with: name: coverage-data pattern: my-artifact-* + include-hidden-files: true coverage: name: Combine coverage diff --git a/README.md b/README.md index 83f5c68..c63c008 100644 --- a/README.md +++ b/README.md @@ -128,9 +128,9 @@ conda env create -f development.yml conda activate readfish_dev ``` -|

‼️ Important !!

| -|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| MinKNOW is transitioning from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.
As of MinKNOW version 5.9 and Dorado server version 7.3.9 and greater Dorado requires an alternate library, `ont-pybasecall-client-lib`.
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. | +|

‼️ Important !!

| +|:------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| MinKNOW has now transitioned from Guppy to Dorado. Until MinKNOW version 5.9 both Guppy and Dorado used ont-pyguppy-client-lib.
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.
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.