bash: cellranger: command not found

[dm8000]

Hello

I followed the installation instructions but I was not able to run any cell ranger command.

When I try this line -with the appropriate path

$ cellranger mkfastq --id=tiny-bcl \
                     --run=/path/to/tiny_bcl \
                     --samplesheet=cellranger-tiny-bcl-samplesheet-1.2.0.csv

I get this

bash: cellranger: command not found

I got no problems when I unpacked the tar in the tutorial.

[diogomoraes@hidden cellranger-7.0.0]$ pwd
/mypath/yard/apps/cellranger-7.0.0
[diogomoraes@hidden cellranger-7.0.0]$ ls
bin             cellranger  lib      mro         sourceme.bash  target_panels
builtwith.json  external    LICENSE  probe_sets  sourceme.csh

[adam-azarchs]

In the instructions there is the line

$ export PATH=/opt/cellranger-7.0.0:$PATH

Which assumes you untarred the tarball in /opt. You will need to add the directory where you actually untarred it into your PATH, or use the full path, in this case

$ export PATH=/mypath/yard/apps/cellranger-7.0.0:$PATH

[dm8000]

thank adam! the issue is solved