problem in install cellranger

Question

[yueli7]

Hello, Everyone,

I cannot install cellranger.

Thanks in advance for any help!

Yue

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/installation

$cd /opt
$tar -xzvf cellranger-3.1.0.tar.gz
$tar -xzvf refdata-cellranger-GRCh38-3.0.0.tar.gz
$export PATH=/opt/cellranger-3.1.0:$path
$cellranger sitecheck > sitecheck.txt
cellranger: command not found

[GenoMax]

Do export PATH=/opt/cellranger-3.1.0:$PATH (note capital PATH) and that should fix the problem.

[yueli7]

Hello, genomax,

Thank you so much for your help!

$ cd /opt
$ export PATH=/opt/cellranger-3.1.0:$PATH
$ cellranger sitecheck > sitecheck.txt
bash: sitecheck.txt: Permission denied

[yueli7]

I also tried:

$ export PATH=/opt/cellranger-3.1.0:$PATH
$ cellranger testrun --id=tiny
cellranger: command not found

Answer 1

[yueli7]

~/opt/cellranger-3.1.0$ export PATH=/opt/cellranger-3.1.0:$PATH
~/opt/cellranger-3.1.0$ vim ~/.bashrc
~/opt/cellranger-3.1.0$ export PATH="~/opt/cellranger-3.1.0:$PATH"