error message during installation of too-many-cells on ubuntu about too-many-cells HOT 22 CLOSED

This issue is solved with newer glib releases. I updated glib here, so pull the new version and try to install again (and let me know if it works).

from too-many-cells.

thanks for your fast response. Installation worked fine, however, when I try the example in R I get this error : "sh: 1: too-many-cells: not found
Error in system2("too-many-cells", args = c(args, autoArgs), stdout = TRUE) :
error in running command
In addition: Warning message:
In dir.create(output, recursive = TRUE) : 'out' already exists"
I should mention that I installed toomanycellsR first and then I installed too-many-cells.

from too-many-cells.

Docker or from source? If using docker, be sure to set the docker argument.

from too-many-cells.

I have both, but I want to use the source.

from too-many-cells.

Is too-many-cells in your path? It should be in ~/.local/bin.

from too-many-cells.

Yes, it is:
Copied executables to /home/zeinab/.local/bin:

• too-many-cells

from too-many-cells.

Is /home/zeinab/.local/bin in your $PATH?

from too-many-cells.

Yes, I double checked, it is in my $PATH list.

from too-many-cells.

Ah, so which too-many-cells is returning a result? I keep bringing this up because sh: 1: too-many-cells: not found means that your shell cannot find the command. If which too-many-cells does return a result, then there must be some disconnect between R and your shell.

from too-many-cells.

It returns"/home/zeinab/.local/bin/too-many-cells". Could you please help me to check the connection between R and the shell?

from too-many-cells.

Interesting. Can you open R in your home folder and run system2("too-many-cells", stdout = TRUE)? Then open R in your ~/.local/bin folder and do the same?

from too-many-cells.

thank you for your help.
both of them return: "Missing: (make-tree | interactive | differential | diversity | paths)

Usage: too-many-cells (make-tree | interactive | differential | diversity |
paths)
character(0)
attr(,"status")
[1] 1
Warning message:
In system2("too-many-cells", stdout = TRUE) :
running command ''too-many-cells'' had status 1
"

from too-many-cells.

So it can find the command in both cases, but in the tooManyCell() function in those same sessions it does not find the command?

from too-many-cells.

That is right! Still I could not solve the issue.

from too-many-cells.

This may be beyond my understanding. The tooManyCells() function uses system2("too-many-cells") with no changing of directories, so I don't know what to do if system2 can find the command line program outside the function but not inside (which should not be happening). My suggestion would be to just call it outside the function or use the command line program.

from too-many-cells.

Thanks for your suggestions. I used the command line for the example data and it worked fine, I am wondering if I provide cytof data in csv format, whether too many cells is accepting that format? Do I need to provide gene names and cell IDs too? Can I send you an example of the csv format that you could examine the format of the file? Thanks in advance.

from too-many-cells.

You can use csv format, just input it with -m data.csv. The format is a normal csv file, with a header for the name of the column (cell) and an initial column containing the features as the first column. With this data, don't forget to change the default normalization and filters (I would recommend something like --normalization UQNorm and -F for no filtering)!

from too-many-cells.

Thank you very much for your help. It works fine.

from too-many-cells.

Hi Gregory,
I am wondering if I provide gene.csv file for the list of features that is measured, how can I point to a specific gene when I want to color the dendrogram based on a gene expression level? thanks

from too-many-cells.

The instructions would be the same as on the website (https://gregoryschwartz.github.io/too-many-cells/) under "gene expression". Although you wouldn't have a "genes" file, you just load in the matrix you used earlier to create the tree.

from too-many-cells.

Thanks for your help.

from too-many-cells.

My pleasure!

from too-many-cells.