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theislab / single-cell-tutorial

Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
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List of package versions for the latest version of the notebook #104

Closed davidecarlson closed 2 years ago

davidecarlson commented 2 years ago

Hi All,

I've been trying to work through the latest version of the single cell tutorial notebook, but I inevitably run into various errors, which I believe are likely caused by having the wrong versions of various packages.

Would it be possible to get a list of all the software versions that were used to successfully run the above-referenced notebook? Similar to the sc_tutorial_environment.yml file, but with the version numbers for each package.

For example, if someone who is able to run the whole notebook successfully from start to finish could run and attach the output of conda env export, that would be super helpful!

Thank you! Dave

davidecarlson commented 2 years ago

Since the R packages would not necessarily be installed by conda, having a list of the specific R package versions would be helpful as well. For example (stolen from here):

ip <- as.data.frame(installed.packages()[,c(1,3:4)])
rownames(ip) <- NULL
ip <- ip[is.na(ip$Priority),1:2,drop=FALSE]
print(ip, row.names=FALSE)

Thanks!

LuckyMD commented 2 years ago

Hi @davidecarlson,

I'm currently travelling, so not able to do the above. However, you can check out the docker image we have generated and run that to export the versions of each package.

davidecarlson commented 2 years ago

Thanks. I was able to get export the package versions from the docker image, and will try to set up my environment based on that.