If macOS is the only choice I would consider running it through Docker. SInce CellRanger itself is fully self-contained you (probably, unested) don't even need to build a container, but just use any Linux container (CentOS, Ubuntu) and run commands from inside there.
Installing Cell Ranger
Hello everyone.
I'm now trying to install Cell Ranger following the tutorial described in 10x genomics website (https://www.10xgenomics.com/jp/support/software/cell-ranger/latest/tutorials/cr-tutorial-in), but facing the problem.
I installed the Cell ranger package (cellranger-8.0.0) and added a path to it as follows;
export PATH=/Users/******/desktop/cellranger_downloads/cellranger-8.0.0:$PATH
I suppose Cell Ranger was successfully added to the $PATH because output of "which cellranger" command seemed proper;
/Users/******/desktop/cellranger_downloads/cellranger-8.0.0/cellranger
However, when I runned "cellranger" command or tried testrun (cellranger testrun --id=tiny), the following error message appeared...
**zsh: exec format error: cellranger**
I'm conducting the experiment using Mac PC (Apple M1 Max).
If anyone knows of a solution, I would appreciate it if you could enlighten me.
Best regards,
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cellranger you downloaded is compiled for Linux. You can't use it as is on macOS. Since celleanger is a closed source application you can't do much about this (i.e. you can't recompile etc).
Consider switching to alevin-fry or starsolo if you do not have access to linux hardware but need to work with single-cell data.
"Running Cell Ranger requires at least 8 CPUs, preferably 16, and at least 64 GB of RAM, preferably 128." - https://www.10xgenomics.com/support/software/cell-ranger/latest/tutorials/cr-tutorial-in
Yeah... meanwhile, all other open source programs take a quarter (or less) of that to run.
Cell Ranger still has useful utilities, like bamtofastq, and so it's still worth installing for certain use cases.
My personal opinion is that scaling / big data and use of laptops are mutually exclusive or at least not a native choice. You will probably need to allocate most of the resources to the Docker VM in such a scenario. On top, be sure to disable all these (useless) additional analysis that CellRanger does (like tSNEs etc, I think flag is something like --no-secondary) to save time and RAM. If you're at a company or university reach out to IT and ask whether any cluste/HPC infrastructures is available that you could use. If not, then it's just wait and see. A "normal" 10x run (say 10k cells, 30k reads/cell) takes some hours on a decent HPC node, so depending on your number of samples that will take time on a laptop.
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You cannot run
cellrangeron a Mac: https://kb.10xgenomics.com/hc/en-us/articles/115003535986-Can-I-run-Cell-Ranger-on-my-Mac-or-Windows-machineIf you do not have access to a GNU/Linux system, the alternatives that I can think of is using
dockerdirectly or switching tonf-core/scrnaseq(https://nf-co.re/scrnaseq/2.5.1) and making use of docker/singularity indirectly.Thank you all for all the advice. I was completely mistaken that the Cell Ranger could be operated in a terminal. I will try the analysis using Docker. If I have any problems, I might have to post question here. Thank you in advance.