Prebuilt docker image? about bayesprism

[tinyi]

Hi William, Sorry for the late reply. I am not entirely sure, but it could be caused by a version issue of scran. I tested 4.2.1 and 4.1.3, and it works. Best, Tinyi

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On Tue, May 23, 2023 at 4:13 PM William C Grisaitis < ***@***.***> wrote: Tinyi, thanks for the reply! I found that devtools::install_github("Danko-Lab/BayesPrism/BayesPrism") didn't work out of the box. I first had to: 1. Install libglpk-dev: sudo apt-get install -y --no-install-recommends libglpk-dev 2. Install bluster and scran with bioconductor: BiocManager::install('bluster'), BiocManager::install('scran') Then everything worked with devtools::install_github("Danko-Lab/BayesPrism/BayesPrism"). Do things work just with devtools::install_github("Danko-Lab/BayesPrism/BayesPrism") for you? Maybe our environments are different in some way. - Perhaps scran is available on a different CRAN mirror? - Also, I am using R 4.3. Maybe scran only has installation candidates on CRAN for older versions of R? — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHS67TMDTH7OMSFJTY63XHUK47ANCNFSM6AAAAAAX33RMBA> . You are receiving this because you commented.Message ID: ***@***.***>

[tinyi]

Hi William, Thank you for your interest in our method. We do not have a docker image yet, as the installation of BayesPrism is relatively straightforward. We are certainly open to having a docker. I suggest you may upload the docker in your fork and let me know, and I can then merge the fork. Best, Tinyi

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On Tue, May 9, 2023 at 5:34 PM William C Grisaitis ***@***.***> wrote: Hi, do you have an official docker image for this? If not, are you open to a pull request for one? I am developing one, and I think this might be useful for some folks. — Reply to this email directly, view it on GitHub <#36>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AB4NHS5IEUKWMVXPRRH34WLXFKZ4ZANCNFSM6AAAAAAX33RMBA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[grisaitis]

Tinyi, thanks for the reply!

I found that devtools::install_github("Danko-Lab/BayesPrism/BayesPrism") didn't work out of the box.

I first had to:

1. Install libglpk-dev: sudo apt-get install -y --no-install-recommends libglpk-dev
2. Install bluster and scran with bioconductor: BiocManager::install('bluster'), BiocManager::install('scran')

Then everything worked with devtools::install_github("Danko-Lab/BayesPrism/BayesPrism").

Do things work just with devtools::install_github("Danko-Lab/BayesPrism/BayesPrism") for you? Maybe our environments are different in some way.

• Perhaps scran is available on a different CRAN mirror?
• Also, I am using R 4.3. Maybe scran only has installation candidates on CRAN for older versions of R?