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Prebuilt docker image?

Open grisaitis opened this issue 2 years ago • 3 comments

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.

grisaitis avatar May 09 '23 21:05 grisaitis

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

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 https://github.com/Danko-Lab/BayesPrism/issues/36, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS5IEUKWMVXPRRH34WLXFKZ4ZANCNFSM6AAAAAAX33RMBA . You are receiving this because you are subscribed to this thread.Message ID: @.***>

tinyi avatar May 10 '23 05:05 tinyi

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?

grisaitis avatar May 23 '23 20:05 grisaitis

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

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 https://github.com/Danko-Lab/BayesPrism/issues/36#issuecomment-1560061917, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB4NHS67TMDTH7OMSFJTY63XHUK47ANCNFSM6AAAAAAX33RMBA . You are receiving this because you commented.Message ID: @.***>

tinyi avatar Jun 07 '23 04:06 tinyi