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problem in install cellranger

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
rna-seq
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written by yueli7 yueli7

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

• 0 views • link
written by GenoMax GenoMax

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
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written by yueli7 yueli7

I also tried:

$ export PATH=/opt/cellranger-3.1.0:$PATH
$ cellranger testrun --id=tiny
cellranger: command not found
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written by yueli7 yueli7

1 answer 

~/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"
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written by yueli7 yueli7

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