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10XGenomics / cellranger

10x Genomics Single Cell Analysis
https://www.10xgenomics.com/support/software/cell-ranger
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What is needed from ./external/? #231

Closed nick-youngblut closed 11 months ago

nick-youngblut commented 1 year ago

Since the ./external/ directory in cellranger-7.1.0 is ~1.5 Gb, I would like to exclude it from my custom Cell Ranger Docker container. However, if one runs cellranger count without the ./external/ directory, then one gets the error:

       Caused by: Failed to run mrg
        Caused by: No such file or directory (os error 2)

What is actually required in the ./external/ directory for running of cellranger count (and other subcommands)? Maybe a fork could be created of cellranger that is a minimal version that is optimized for Docker containers (e.g., a cellranger-slim version)? The cellranger-7.1.0 codebase is nearly 2 Gb when uncompressed.

Maybe anaconda can be replaced with micromamba?

elehnert10x commented 11 months ago

Thank you for your interest in Cell Ranger. GitHub Issues are not monitored by our support team. Please e-mail support@10xgenomics.com for support with Cell Ranger or visit our documentation site at https://www.10xgenomics.com/support/software/cell-ranger.

nick-youngblut commented 10 months ago

GitHub Issues are not monitored by our support team

Thanks @elehnert10x for the info. It might be helpful to put that info in the issue template for this repo.

elehnert10x commented 10 months ago

Thank you for your understanding. We will be making that more clear - we wanted to respond and provide recent inquiries a path forward before making those changes.