Question: CellRanger installation question
0
gravatar for whguusa
4 months ago by
whguusa0
whguusa0 wrote:

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

software error • 375 views
ADD COMMENTlink modified 16 days ago by priyankasubmissions0270 • written 4 months ago by whguusa0

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

ADD REPLYlink modified 16 days ago • written 17 days ago by Fatima350

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

ADD REPLYlink modified 16 days ago • written 16 days ago by Arup Ghosh2.1k
0
gravatar for genomax
4 months ago by
genomax78k
United States
genomax78k wrote:

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.

ADD COMMENTlink written 4 months ago by genomax78k

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

ADD REPLYlink written 16 days ago by Fatima350

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

ADD REPLYlink modified 16 days ago • written 16 days ago by genomax78k

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.

ADD REPLYlink modified 16 days ago • written 16 days ago by Fatima350

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

ADD REPLYlink written 16 days ago by genomax78k
0
gravatar for Fatima
16 days ago by
Fatima350
United states
Fatima350 wrote:

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

ADD COMMENTlink written 16 days ago by Fatima350
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