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romanhaa / Cerebro

Visualization of scRNA-seq data.
MIT License
93 stars 19 forks source link

Error: cannot add bindings to a locked environment #29

Open ccruizm opened 3 years ago

ccruizm commented 3 years ago

Good day,

Thanks for developing such a great tool. I have created my .crb file in our HPC and downloaded it to my laptop where I download the Cerebro app. However, when loading the dataset, I get an error. What can be the cause of this problem? I have the impression that this is a standalone app that can run independently (I do not have R installed on my local computer).

Thanks in advance for your help!

Screenshot 2020-12-16 at 17 44 04
ccruizm commented 3 years ago

Sorry, after I carefully reading of other issues and the web app, my problem is likely due to the version I used to generate my crb file (v1.3). Unfortunately, I can not use the shiny app because I run R in a jupyter notebook on our HPC and haven't been able to use any shiny apps in that setting (if maybe you have any ideas of how-to, I will greatly appreciate it)

It seems I have to be patient until the new app is released! looking forward to it

romanhaa commented 3 years ago

Can you install cerebroApp (the R package) on your local machine? I think that would be the easiest solution. You could then generate the .crb file with v1.3 on the HPC, transfer it to your local machine and load it into Cerebro v1.3 that you launch from within R using this function.

Sirt0r commented 3 years ago

I also have the same problem. For myself I would like to use Cerebro to help others from my team to interact with these types of analyses on our own server. So If I try to load the .crb file in my R session, it works perfectly fine. However it does not on the server with installed via docker. Do you think you could look at your docker container again?

romanhaa commented 3 years ago

Right, there is no Docker container with cerebroApp v.1.3 installed in it. The most recent is based on v1.2.2. I will try to get around creating one this weekend.

romanhaa commented 3 years ago

Quick update: There is now a Docker image running Cerebro v1.3.0. You can find it here with tag v1.3.0_light (light because it only contains cerebroApp and not Seurat, so you can't use it for analysis). The latest tag refers to the same image. You can launch a container like this: docker run -it -p 8080:8080 --rm romanhaa/cerebro:v1.3.0

Let me know if that helps.

Sirt0r commented 3 years ago

Perfect. It runs smoothly now and I can view the files through the server. Thank you very much.

ccruizm commented 3 years ago

I have tried to use the docker image but our server does not have installed Docker for security reasons and we use singularity. I could not find how to do port forwarding using singularity. Do you have maybe any ideas on how I could do this, please? btw, any news on the portable app? that would be a huge help (and easier to share for people with no bioinformatics background)!

Thanks!