CellRanger installation question

Question

[whguusa]

Hi,

I was trying to instal CellRanger on my Mac (10.12.5), I followed the tutorial here (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation ).

Download and unpack were good, but cannot invoke the cellranger command.

I run this line:

export PATH=Path2UnpackedFile/cellranger-3.1.0:$PATH

And the error is:

readlink: illegal option -- f usage: readlink [-n] [file ...] usage: dirname path /Users/MyUserName/CellRanger/cellranger-3.1.0/cellranger: line 31: /../tenkit/bin/common/_master: No such file or directory

Thus I cannot run cellranger command.

I wonder what is missing.

Thank you so much!

Best

[Fatima]

You can find the path by running pwd while in cellranger-3.1.0 folder. If pwd returns /home/opt/cellranger-3.1.0 then

export PATH=/home/opt/cellranger-3.1.0:$PATH

The / before path is necessary

[Arup Ghosh]

Make sure you are using the complete and correct path to the Cellranger directory and make sure every entry in .bashrc file is valid.

Answer 1

[GenoMax]

macOS is not equivalent to Linux.

Page you linked has binaries/files that work on Linux distributions. You will not be able to run them as is on your Mac. You may be able to run them using a virtual machine that runs linux.

[Fatima]

Mac terminal can process unix commands and should be able to run binary files.

[GenoMax]

That is NOT correct. Even though macOS is BSD based it is not binary compatible with linux.

[Fatima]

Yes, you are right, but we also have binaries designed for MacOS. I misunderstood your original comment, now that I read it again I know what you mean.

[GenoMax]

10x only supports linux and since they only make binaries available there is no native support for macOS.

[sxs870917]

Here is the link: https://kb.10xgenomics.com/hc/en-us/articles/115003535986-Can-I-run-Cell-Ranger-on-my-Mac-or-Windows-machine-

Question: Can I run Cell Ranger on my Mac or Windows machine?

Answer: No, Cell Ranger only runs on Linux systems. Please see Cell Ranger System Requirements.

However, the visualization software Loupe Cell Browser runs on both macOS and Windows. For more information on Loupe Cell Browser, please see Loupe Cell Browser Downloads.

You can explore the functionality of Loupe Cell Browser by downloading example .cloupe files from publicly available 10x datasets: Single-Cell Gene Expression Datasets

More information on the single cell gene expression software solutions can be found on our support site.

Answer 2

[Fatima]

If you can run the following command with no errors

./cellranger-cs/3.1.0/bin/cellranger

Then try

rm -f cellranger 
ln -s cellranger-cs/3.1.0/bin/cellranger cellranger

If the command doesn't work, please check this post:

problem in install cellranger